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- PDB-5fci: Structure of the vacant uL3 W255C mutant 80S yeast ribosome -

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Basic information

Entry
Database: PDB / ID: 5fci
TitleStructure of the vacant uL3 W255C mutant 80S yeast ribosome
Components
  • (40S ribosomal protein ...) x 33
  • (60S ribosomal protein ...) x 43
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Suppressor protein STM1,Suppressor protein STM1
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / uL3 mutant / Vacant
Function / homology
Function and homology information


triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / regulation of polysaccharide biosynthetic process / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / nonfunctional rRNA decay / transporter complex / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / telomeric DNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / lipopolysaccharide transport / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of translational frameshifting / TOR signaling / Formation of a pool of free 40S subunits / positive regulation of protein kinase activity / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / Gram-negative-bacterium-type cell outer membrane assembly / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / ribosomal subunit export from nucleus / regulation of translational fidelity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translational termination / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / translation regulator activity / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / telomere maintenance / cellular response to amino acid starvation / protein kinase C binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / macroautophagy / translational initiation / small-subunit processome / modification-dependent protein catabolic process / protein tag activity / maintenance of translational fidelity / cell outer membrane / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus
Similarity search - Function
Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / LptD, C-terminal / LPS-assembly protein LptD / : ...Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Group II dsDNA virus coat/capsid protein / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L13e / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e / 40S Ribosomal protein S10 / : / Ribosomal protein L44e signature. / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19, eukaryotic / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / : / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L44e / Ribosomal protein S3Ae, conserved site / Ribosomal protein L44 / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S27a / Ribosomal protein L34e, conserved site / Ribosomal protein S27a / Ribosomal protein L34e signature. / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L18 C-terminal region / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L23/L25, N-terminal / :
Similarity search - Domain/homology
osmium (III) hexammine / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 ...osmium (III) hexammine / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein uL4A / Putative major capsid protein p72 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Suppressor protein STM1 / Small ribosomal subunit protein eS26A / Small ribosomal subunit protein eS26B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / LPS-assembly protein LptD / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMailliot, J. / Garreau de Loubresse, N. / Yusupova, G. / Dinman, J.D. / Yusupov, M.
Funding support France, Russian Federation, United States, 6items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BCV8-006 01 France
European Research Council294312
Human Frontier Science ProgramRGP0062/2012
Russian Government Program of Competitive Growth of Kazan Federal University Russian Federation
National Institutes of HealthR01GM117177 United States
National Institutes of HealthR01HL119439 United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Crystal Structures of the uL3 Mutant Ribosome: Illustration of the Importance of Ribosomal Proteins for Translation Efficiency.
Authors: Mailliot, J. / Garreau de Loubresse, N. / Yusupova, G. / Meskauskas, A. / Dinman, J.D. / Yusupov, M.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id
Revision 2.1Oct 26, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly_gen ...database_2 / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: 18S ribosomal RNA
S0: 40S ribosomal protein S0-A
S1: 40S ribosomal protein S1-A
S2: 40S ribosomal protein S2
S3: 40S ribosomal protein S3
S4: 40S ribosomal protein S4-A
S5: 40S ribosomal protein S5
S6: 40S ribosomal protein S6-A
S7: 40S ribosomal protein S7-A
S8: 40S ribosomal protein S8-A
S9: 40S ribosomal protein S9-A
C0: 40S ribosomal protein S10-A
C1: 40S ribosomal protein S11-A,40S ribosomal protein S11-A (uS17)
C2: 40S ribosomal protein S12
C3: 40S ribosomal protein S13
C4: 40S ribosomal protein S14-A
C5: 40S ribosomal protein S15
C6: 40S ribosomal protein S16-A
C7: 40S ribosomal protein S17-A
C8: 40S ribosomal protein S18-A
C9: 40S ribosomal protein S19-A
D0: 40S ribosomal protein S20
D1: 40S ribosomal protein S21-A
D2: 40S ribosomal protein S22-A
D3: 40S ribosomal protein S23-A
D4: 40S ribosomal protein S24-A
D5: 40S ribosomal protein S25-A
D6: 40S ribosomal protein S26-A
D7: 40S ribosomal protein S27-A
D8: 40S ribosomal protein S28-A
D9: 40S ribosomal protein S29-A
E0: 40S ribosomal protein S30-A
E1: 40S ribosomal protein S31
SR: Guanine nucleotide-binding protein subunit beta-like protein
SM: Suppressor protein STM1,Suppressor protein STM1
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
L2: 60S ribosomal protein L2-A
L3: 60S ribosomal protein L3
L4: 60S ribosomal protein L4-A
L5: 60S ribosomal protein L5
L6: 60S ribosomal protein L6-A
L7: 60S ribosomal protein L7-A
L8: 60S ribosomal protein L8-A
L9: 60S ribosomal protein L9-A
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11-A
M3: 60S ribosomal protein L13-A
M4: 60S ribosomal protein L14-A
M5: 60S ribosomal protein L15-A
M6: 60S ribosomal protein L16-A
M7: 60S ribosomal protein L17-A
M8: 60S ribosomal protein L18-A
M9: 60S ribosomal protein L19-A
N0: 60S ribosomal protein L20-A
N1: 60S ribosomal protein L21-A
N2: 60S ribosomal protein L22-A
N3: 60S ribosomal protein L23-A
N4: 60S ribosomal protein L24-A
N5: 60S ribosomal protein L25
N6: 60S ribosomal protein L26-A
N7: 60S ribosomal protein L27-A
N8: 60S ribosomal protein L28
N9: 60S ribosomal protein L29
O0: 60S ribosomal protein L30
O1: 60S ribosomal protein L31-A
O2: 60S ribosomal protein L32
O3: 60S ribosomal protein L33-A
O4: 60S ribosomal protein L34-A
O5: 60S ribosomal protein L35-A
O6: 60S ribosomal protein L36-A
O7: 60S ribosomal protein L37-A
O8: 60S ribosomal protein L38
O9: 60S ribosomal protein L39
Q0: Ubiquitin-60S ribosomal protein L40
Q1: 60S ribosomal protein L41-A
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
6: 18S ribosomal RNA
s0: 40S ribosomal protein S0-A
s1: 40S ribosomal protein S1-A
s2: 40S ribosomal protein S2
s3: 40S ribosomal protein S3
s4: 40S ribosomal protein S4-A
s5: 40S ribosomal protein S5
s6: 40S ribosomal protein S6-A
s7: 40S ribosomal protein S7-A
s8: 40S ribosomal protein S8-A
s9: 40S ribosomal protein S9-A
c0: 40S ribosomal protein S10-A
c1: 40S ribosomal protein S11-A,40S ribosomal protein S11-A (uS17)
c2: 40S ribosomal protein S12
c3: 40S ribosomal protein S13
c4: 40S ribosomal protein S14-A
c5: 40S ribosomal protein S15
c6: 40S ribosomal protein S16-A
c7: 40S ribosomal protein S17-A
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: 40S ribosomal protein S20
d1: 40S ribosomal protein S21-A
d2: 40S ribosomal protein S22-A
d3: 40S ribosomal protein S23-A
d4: 40S ribosomal protein S24-A
d5: 40S ribosomal protein S25-A
d6: 40S ribosomal protein S26-A
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
e0: 40S ribosomal protein S30-A
e1: 40S ribosomal protein S31
sR: Guanine nucleotide-binding protein subunit beta-like protein
sM: Suppressor protein STM1,Suppressor protein STM1
5: 25S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
l2: 60S ribosomal protein L2-A
l3: 60S ribosomal protein L3
l4: 60S ribosomal protein L4-A
l5: 60S ribosomal protein L5
l6: 60S ribosomal protein L6-A
l7: 60S ribosomal protein L7-A
l8: 60S ribosomal protein L8-A
l9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-A
m2: 60S ribosomal protein L12-A (uL11)
m3: 60S ribosomal protein L13-A
m4: 60S ribosomal protein L14-A
m5: 60S ribosomal protein L15-A
m6: 60S ribosomal protein L16-A
m7: 60S ribosomal protein L17-A
m8: 60S ribosomal protein L18-A
m9: 60S ribosomal protein L19-A
n0: 60S ribosomal protein L20-A
n1: 60S ribosomal protein L21-A
n2: 60S ribosomal protein L22-A
n3: 60S ribosomal protein L23-A
n4: 60S ribosomal protein L24-A
n5: 60S ribosomal protein L25
n6: 60S ribosomal protein L26-A
n7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
o0: 60S ribosomal protein L30
o1: 60S ribosomal protein L31-A
o2: 60S ribosomal protein L32
o3: 60S ribosomal protein L33-A
o4: 60S ribosomal protein L34-A
o5: 60S ribosomal protein L35-A
o6: 60S ribosomal protein L36-A
o7: 60S ribosomal protein L37-A
o8: 60S ribosomal protein L38
o9: 60S ribosomal protein L39
q0: Ubiquitin-60S ribosomal protein L40
q1: 60S ribosomal protein L41-A
q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
p0: 60S acidic ribosomal protein P0
p1: 60S ribosomal protein P1 alpha
p2: 60S ribosomal protein P2 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,586,4242465
Polymers6,244,408162
Non-polymers342,0152303
Water00
1
2: 18S ribosomal RNA
S0: 40S ribosomal protein S0-A
S1: 40S ribosomal protein S1-A
S2: 40S ribosomal protein S2
S3: 40S ribosomal protein S3
S4: 40S ribosomal protein S4-A
S5: 40S ribosomal protein S5
S6: 40S ribosomal protein S6-A
S7: 40S ribosomal protein S7-A
S8: 40S ribosomal protein S8-A
S9: 40S ribosomal protein S9-A
C0: 40S ribosomal protein S10-A
C1: 40S ribosomal protein S11-A,40S ribosomal protein S11-A (uS17)
C2: 40S ribosomal protein S12
C3: 40S ribosomal protein S13
C4: 40S ribosomal protein S14-A
C5: 40S ribosomal protein S15
C6: 40S ribosomal protein S16-A
C7: 40S ribosomal protein S17-A
C8: 40S ribosomal protein S18-A
C9: 40S ribosomal protein S19-A
D0: 40S ribosomal protein S20
D1: 40S ribosomal protein S21-A
D2: 40S ribosomal protein S22-A
D3: 40S ribosomal protein S23-A
D4: 40S ribosomal protein S24-A
D5: 40S ribosomal protein S25-A
D6: 40S ribosomal protein S26-A
D7: 40S ribosomal protein S27-A
D8: 40S ribosomal protein S28-A
D9: 40S ribosomal protein S29-A
E0: 40S ribosomal protein S30-A
E1: 40S ribosomal protein S31
SR: Guanine nucleotide-binding protein subunit beta-like protein
SM: Suppressor protein STM1,Suppressor protein STM1
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
L2: 60S ribosomal protein L2-A
L3: 60S ribosomal protein L3
L4: 60S ribosomal protein L4-A
L5: 60S ribosomal protein L5
L6: 60S ribosomal protein L6-A
L7: 60S ribosomal protein L7-A
L8: 60S ribosomal protein L8-A
L9: 60S ribosomal protein L9-A
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11-A
M3: 60S ribosomal protein L13-A
M4: 60S ribosomal protein L14-A
M5: 60S ribosomal protein L15-A
M6: 60S ribosomal protein L16-A
M7: 60S ribosomal protein L17-A
M8: 60S ribosomal protein L18-A
M9: 60S ribosomal protein L19-A
N0: 60S ribosomal protein L20-A
N1: 60S ribosomal protein L21-A
N2: 60S ribosomal protein L22-A
N3: 60S ribosomal protein L23-A
N4: 60S ribosomal protein L24-A
N5: 60S ribosomal protein L25
N6: 60S ribosomal protein L26-A
N7: 60S ribosomal protein L27-A
N8: 60S ribosomal protein L28
N9: 60S ribosomal protein L29
O0: 60S ribosomal protein L30
O1: 60S ribosomal protein L31-A
O2: 60S ribosomal protein L32
O3: 60S ribosomal protein L33-A
O4: 60S ribosomal protein L34-A
O5: 60S ribosomal protein L35-A
O6: 60S ribosomal protein L36-A
O7: 60S ribosomal protein L37-A
O8: 60S ribosomal protein L38
O9: 60S ribosomal protein L39
Q0: Ubiquitin-60S ribosomal protein L40
Q1: 60S ribosomal protein L41-A
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
5: 25S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,468,5191956
Polymers4,193,55380
Non-polymers274,9651876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
6: 18S ribosomal RNA
s0: 40S ribosomal protein S0-A
s1: 40S ribosomal protein S1-A
s2: 40S ribosomal protein S2
s3: 40S ribosomal protein S3
s4: 40S ribosomal protein S4-A
s5: 40S ribosomal protein S5
s6: 40S ribosomal protein S6-A
s7: 40S ribosomal protein S7-A
s8: 40S ribosomal protein S8-A
s9: 40S ribosomal protein S9-A
c0: 40S ribosomal protein S10-A
c1: 40S ribosomal protein S11-A,40S ribosomal protein S11-A (uS17)
c2: 40S ribosomal protein S12
c3: 40S ribosomal protein S13
c4: 40S ribosomal protein S14-A
c5: 40S ribosomal protein S15
c6: 40S ribosomal protein S16-A
c7: 40S ribosomal protein S17-A
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: 40S ribosomal protein S20
d1: 40S ribosomal protein S21-A
d2: 40S ribosomal protein S22-A
d3: 40S ribosomal protein S23-A
d4: 40S ribosomal protein S24-A
d5: 40S ribosomal protein S25-A
d6: 40S ribosomal protein S26-A
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
e0: 40S ribosomal protein S30-A
e1: 40S ribosomal protein S31
sR: Guanine nucleotide-binding protein subunit beta-like protein
sM: Suppressor protein STM1,Suppressor protein STM1
5: 25S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
l2: 60S ribosomal protein L2-A
l3: 60S ribosomal protein L3
l4: 60S ribosomal protein L4-A
l5: 60S ribosomal protein L5
l6: 60S ribosomal protein L6-A
l7: 60S ribosomal protein L7-A
l8: 60S ribosomal protein L8-A
l9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-A
m2: 60S ribosomal protein L12-A (uL11)
m3: 60S ribosomal protein L13-A
m4: 60S ribosomal protein L14-A
m5: 60S ribosomal protein L15-A
m6: 60S ribosomal protein L16-A
m7: 60S ribosomal protein L17-A
m8: 60S ribosomal protein L18-A
m9: 60S ribosomal protein L19-A
n0: 60S ribosomal protein L20-A
n1: 60S ribosomal protein L21-A
n2: 60S ribosomal protein L22-A
n3: 60S ribosomal protein L23-A
n4: 60S ribosomal protein L24-A
n5: 60S ribosomal protein L25
n6: 60S ribosomal protein L26-A
n7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
o0: 60S ribosomal protein L30
o1: 60S ribosomal protein L31-A
o2: 60S ribosomal protein L32
o3: 60S ribosomal protein L33-A
o4: 60S ribosomal protein L34-A
o5: 60S ribosomal protein L35-A
o6: 60S ribosomal protein L36-A
o7: 60S ribosomal protein L37-A
o8: 60S ribosomal protein L38
o9: 60S ribosomal protein L39
q0: Ubiquitin-60S ribosomal protein L40
q1: 60S ribosomal protein L41-A
q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
p0: 60S acidic ribosomal protein P0
p1: 60S ribosomal protein P1 alpha
p2: 60S ribosomal protein P2 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,324,7381278
Polymers3,148,34983
Non-polymers176,3891195
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)435.450, 287.660, 303.760
Angle α, β, γ (deg.)90.000, 98.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 4 types, 8 molecules 26153748

#1: RNA chain 18S ribosomal RNA / Saccharomyces cerevisiae S288c RDN37-1 miscRNA


Mass: 579761.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: REF: 831416132
#36: RNA chain 25S ribosomal RNA / Saccharomyces cerevisiae S288c RDN37-1 miscRNA


Mass: 1097493.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: REF: 831416132
#37: RNA chain 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 834774822
#38: RNA chain 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 940534893

+
40S ribosomal protein ... , 33 types, 64 molecules S0s0S1s1S2s2S3s3S4s4S5s5S6s6S7s7S8s8S9s9C0C1c1C2c2C3c3C4c4C5...

#2: Protein 40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A


Mass: 27920.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P32905
#3: Protein 40S ribosomal protein S1-A / RP10A


Mass: 28667.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P33442
#4: Protein 40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


Mass: 27359.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P25443
#5: Protein 40S ribosomal protein S3 / RP13 / YS3


Mass: 26411.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05750
#6: Protein 40S ribosomal protein S4-A / RP5 / S7 / YS6


Mass: 29338.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX35
#7: Protein 40S ribosomal protein S5 / RP14 / S2 / YS8


Mass: 24941.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P26783
#8: Protein 40S ribosomal protein S6-A / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX37
#9: Protein 40S ribosomal protein S7-A / RP30 / RP40


Mass: 21527.014 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P26786
#10: Protein 40S ribosomal protein S8-A / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX39
#11: Protein 40S ribosomal protein S9-A / RP21 / S13 / YP28 / YS11


Mass: 22356.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: O13516
#12: Protein 40S ribosomal protein S10-A


Mass: 12785.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Remaining misalignments result from differences in the distribution of (UNK)s between the two instances of the molecule in the structure. Here is the original sequence ot the crystallized protein : MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFSWQYYYYTLTEEGVEYLREYL NLPEHIVPATYIQERNPTQRPQRRY
Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q08745
#13: Protein 40S ribosomal protein S11-A,40S ribosomal protein S11-A (uS17) / RP41 / S18 / YS12


Mass: 17354.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Remaining misalignments result from differences in the distribution of (UNK)s between the two instances of the molecule in the structure. Here is the original sequence ot the crystallized protein : STELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPFTGLVSIRGKILTGTVVSTKMH RTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQCRPISKTVRFNVVKVSAAAAKANKQFAKF
Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX47
#14: Protein 40S ribosomal protein S12


Mass: 14962.108 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Remaining misalignments result from differences in the distribution of (UNK)s between the two instances of the molecule in the structure. Here is the original sequence ot the crystallized protein : SDVEEVVEVQEETVVEQTAEVTIEDALKVVLRTALVHDGLARGLRESTKALTRGEALLVVLVSSVTEANIIKLVEGLAND PENKVPLIKVADAKQLGEWAGLAKIDREANARKVVGASVVVVKNWGAETDELSMIMEHFSQQ
Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P48589
#15: Protein 40S ribosomal protein S13 / S27a / YS15


Mass: 16928.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05756
#16: Protein 40S ribosomal protein S14-A / RP59A


Mass: 14431.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Remaining misalignments result from differences in the distribution of (UNK)s between the two instances of the molecule in the structure. Here is the original sequence ot the crystallized protein : SNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAMLAAQDVAAKCKEVGITAVHV KIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPVPSDSTRKKGGRRGRRL
Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P06367
#17: Protein 40S ribosomal protein S15 / RIG protein / RP52 / S21 / YS21


Mass: 15900.712 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Remaining misalignments result from differences in the distribution of (UNK)s between the two instances of the molecule in the structure. Here is the original sequence ot the crystallized protein : SQAVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEKPAPVRTHMR NMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHGRAGATTSRFIPLK
Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q01855
#18: Protein 40S ribosomal protein S16-A / RP61R


Mass: 15746.292 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX51
#19: Protein 40S ribosomal protein S17-A / RP51A


Mass: 15820.413 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P02407
#20: Protein 40S ribosomal protein S18-A


Mass: 16940.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX55
#21: Protein 40S ribosomal protein S19-A / RP55A / S16a / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P07280
#22: Protein 40S ribosomal protein S20


Mass: 13797.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38701
#23: Protein 40S ribosomal protein S21-A / S26 / YS25


Mass: 9758.829 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0C0V8
#24: Protein 40S ribosomal protein S22-A / RP50 / S24 / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0C0W1
#25: Protein 40S ribosomal protein S23-A / RP37 / S28 / YS14


Mass: 15942.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX29
#26: Protein 40S ribosomal protein S24-A / RP50


Mass: 15231.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX31
#27: Protein 40S ribosomal protein S25-A / RP45 / S31 / YS23


Mass: 11936.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q3E792
#28: Protein 40S ribosomal protein S26-A


Mass: 11022.989 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P39938, UniProt: P39939*PLUS
#29: Protein 40S ribosomal protein S27-A / RP61 / YS20


Mass: 8762.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P35997
#30: Protein 40S ribosomal protein S28-A / S33 / YS27


Mass: 7474.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q3E7X9
#31: Protein 40S ribosomal protein S29-A / S36 / YS29


Mass: 6544.527 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P41057
#32: Protein 40S ribosomal protein S30-A


Mass: 7006.346 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX33
#33: Protein 40S ribosomal protein S31


Mass: 8703.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05759
#80: Protein 40S ribosomal protein S10-A


Mass: 11181.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Remaining misalignments result from differences in the distribution of (UNK)s between the two instances of the molecule in the structure. Here is the original sequence ot the crystallized protein : MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFSWQYYYYTLTEEGVEYLREYL NLPEHIVPATYIQERNPTQRPQRRY
Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q08745

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Protein , 4 types, 7 molecules SRsRSMsMQ0q0p0

#34: Protein Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 34710.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38011
#35: Protein Suppressor protein STM1,Suppressor protein STM1 / 3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / ...3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / Ribosomal subunits association factor / AF / TOM1 suppressor protein 1 / Triplex-binding protein 1


Mass: 18715.916 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Remaining misalignments result from differences in the distribution of (UNK)s between the two instances of the molecule in the structure. Here is the original sequence ot the crystallized protein : MSNPFDLLGNDVEDADVVVLPPKEIVKSNTSSKKADVPPPSADPSKARKNRPRPSGNEGAIRDKTAGRRNNRSKDVTDSA TTKKSNTRRATDRHSRTGKTDTKKKVNQGWGDDKKELSAEKEAQADAAAEIAEDAAEAEDAGKPKTAQLSLQDYLNQQAN NQFNKVPEAKKVELDAERIETAEKEAYVPATKVKNVKSKQLKTKEYLEFDATFVESNTRKNFGDRNNNSRNNFNNRRGGR GARKGNNTANATNSANTVQKNRNIDVSNLPSLA
Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P39015
#76: Protein Ubiquitin-60S ribosomal protein L40


Mass: 6032.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CH08
#82: Protein 60S acidic ribosomal protein P0 / A0 / L10E


Mass: 33158.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Here is the original sequence ot the crystallized protein : GGIREKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKLLPFVK GNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRAVNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDA GNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQVFPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLIN NYKDLLAVAIAASYHYPEIEDLVDRIENPEKYAAAAPAATSAASGDAAPAEEAAAEEEEESDDDMGFGLFD
Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05317

+
60S ribosomal protein ... , 43 types, 83 molecules L2l2L3l3L4l4L5l5L6l6L7l7L8l8L9l9M0m0M1m1M3m3M4m4M5m5M6m6M7m7...

#39: Protein 60S ribosomal protein L2-A / L5 / RP8 / YL6


Mass: 27332.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX45
#40: Protein 60S ribosomal protein L3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43636.531 Da / Num. of mol.: 2 / Mutation: W255C / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P14126
#41: Protein 60S ribosomal protein L4-A / L2 / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P10664
#42: Protein 60S ribosomal protein L5 / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33633.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P26321
#43: Protein 60S ribosomal protein L6-A / L17 / RP18 / YL16


Mass: 19869.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q02326
#44: Protein 60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 27555.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05737
#45: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28044.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Remaining misalignments result from differences in the distribution of (UNK)s between the two instances of the molecule in the structure. Here is the original sequence ot the crystallized protein : APGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPPTIAQFQYT LDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEAKSKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIE LVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGNK AQAKMDKRAKNSDSA
Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P17076
#46: Protein 60S ribosomal protein L9-A / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05738
#47: Protein 60S ribosomal protein L10 / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25279.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P41805
#48: Protein 60S ribosomal protein L11-A / L16 / RP39 / YL22


Mass: 19624.494 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0C0W9
#49: Protein 60S ribosomal protein L13-A


Mass: 22472.967 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q12690
#50: Protein 60S ribosomal protein L14-A


Mass: 15063.870 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P36105
#51: Protein 60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05748
#52: Protein 60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15


Mass: 22116.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P26784
#53: Protein 60S ribosomal protein L17-A / L20A / YL17


Mass: 20458.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05740
#54: Protein 60S ribosomal protein L18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX49
#55: Protein 60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX82
#56: Protein 60S ribosomal protein L20-A / L18a


Mass: 20478.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX23
#57: Protein 60S ribosomal protein L21-A


Mass: 18148.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q02753
#58: Protein 60S ribosomal protein L22-A / L1c / RP4 / YL31


Mass: 13580.163 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05749
#59: Protein 60S ribosomal protein L23-A / L17a / YL32


Mass: 14362.755 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX41
#60: Protein 60S ribosomal protein L24-A / L30 / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P04449
#61: Protein 60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 15656.417 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P04456
#62: Protein 60S ribosomal protein L26-A / L33 / YL33


Mass: 14134.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05743
#63: Protein 60S ribosomal protein L27-A


Mass: 15437.166 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0C2H6
#64: Protein 60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P02406
#65: Protein 60S ribosomal protein L29 / YL43


Mass: 6560.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05747
#66: Protein 60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 11299.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P14120
#67: Protein 60S ribosomal protein L31-A / L34 / YL28


Mass: 12848.962 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0C2H8
#68: Protein 60S ribosomal protein L32


Mass: 14678.246 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38061
#69: Protein 60S ribosomal protein L33-A / L37 / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05744
#70: Protein 60S ribosomal protein L34-A


Mass: 13542.001 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P87262
#71: Protein 60S ribosomal protein L35-A


Mass: 13811.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX84
#72: Protein 60S ribosomal protein L36-A / L39 / YL39


Mass: 11020.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05745
#73: Protein 60S ribosomal protein L37-A / L43 / YL35 / YP55


Mass: 9746.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P49166
#74: Protein 60S ribosomal protein L38


Mass: 8714.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P49167
#75: Protein/peptide 60S ribosomal protein L39 / L46 / YL40


Mass: 6227.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P04650
#77: Protein/peptide 60S ribosomal protein L41-A / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX86
#78: Protein 60S ribosomal protein L42-A / L41 / YL27 / YP44


Mass: 12115.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX27
#79: Protein 60S ribosomal protein L43-A / L37a / YL35


Mass: 9981.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CX25
#81: Protein 60S ribosomal protein L12-A (uL11)


Mass: 12783.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Here is the original sequence ot the crystallized protein : MPPKFDPNEVKYLYLRAVGGEVGASAALAPKIGPLGLSPKKVGEDIAKATKEFKGIKVTV QLKIQNRQAAASVVPSASSLVITALKEPPRDRKKDKNVKHSGNIQLDEIIEIARQMRDKS FGRTLASVTKEILGTAQSVGCRVDFKNPHDIIEGINAGEIEIPEN
Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#83: Protein/peptide 60S ribosomal protein P1 alpha


Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Here is the original sequence ot the crystallized protein : MSTESALSYAALILADSEIEISSEKLLTLTNAANVPVENIWADIFAKALDGQNLKDLLVN FSAGAAAPAGVAGGVAGGEAGEAEAEKEEEEAKEESDDDMGFGLFD
Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#84: Protein/peptide 60S ribosomal protein P2 beta


Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Here is the original sequence ot the crystallized protein : MSTESALSYAALILADSEIEISSEKLLTLTNAANVPVENIWADIFAKALDGQNLKDLLVN FSAGAAAPAGVAGGVAGGEAGEAEAEKEEEEAKEESDDDMGFGLFD
Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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Non-polymers , 3 types, 2303 molecules

#85: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 1089 / Source method: obtained synthetically / Formula: H12N6Os
#86: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1198 / Source method: obtained synthetically / Formula: Mg
#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.15873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15873 Å / Relative weight: 1
ReflectionResolution: 3.4→49.993 Å / Num. obs: 1009263 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 89.08 Å2 / Rmerge F obs: 0.975 / Rmerge(I) obs: 0.348 / Rrim(I) all: 0.382 / Χ2: 0.865 / Net I/σ(I): 5.32 / Num. measured all: 4845359
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.4-3.50.3631.4131.0229616483904838631.669100
3.5-3.60.4751.0971.326566074895748471.29499.9
3.6-3.70.5620.8961.623380566976669181.06199.9
3.7-3.80.6310.7391.9220080460108600070.88399.8
3.8-3.90.7240.6082.3718998554176541320.7299.9
3.9-40.7790.5172.7817300648848487790.6199.9
4-50.9080.2964.5610479873024433021290.35199.9
5-60.9670.1587.444714101340261338920.18799.9
6-70.9450.7128.7966581968223682190.751100
7-80.9680.50911.1643427638375383660.534100
8-90.980.36512.7325784323228232210.383100
9-100.9880.2714.9416895014870148720.283100
10-200.9930.16818.3539044735218352060.176100
20-300.9970.07827.7138961361836160.08299.9
30-400.9920.07233.1188138868830.07699.7
400.9920.1098.3414296803130.12446

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V88

4v88


Resolution: 3.4→49.993 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 39095 2 %
Rwork0.2343 1916337 -
obs0.2353 1955432 97.65 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 550 Å2 / Biso mean: 78.4438 Å2 / Biso min: 17.89 Å2
Refinement stepCycle: final / Resolution: 3.4→49.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms180119 222782 8837 0 411738
Biso mean--106.87 --
Num. residues----33337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01439103
X-RAY DIFFRACTIONf_angle_d1.319651275
X-RAY DIFFRACTIONf_chiral_restr0.05379636
X-RAY DIFFRACTIONf_plane_restr0.00641863
X-RAY DIFFRACTIONf_dihedral_angle_d18.741195503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.43860.372412420.3408609066214893
3.4386-3.4790.348612970.318632916458897
3.479-3.52150.359713030.3172635146481797
3.5215-3.5660.338113080.3062636786498697
3.566-3.61290.341912930.3023638696516298
3.6129-3.66240.329313090.2924640496535898
3.6624-3.71470.338113090.2968639506525998
3.7147-3.77020.330913000.286638536515398
3.7702-3.8290.323112970.2782639606525798
3.829-3.89180.320213220.2679645776589999
3.8918-3.95890.298513020.2505641726547498
3.9589-4.03080.301213050.2504639516525698
4.0308-4.10830.301412940.2457634216471597
4.1083-4.19210.299512760.2448623206359695
4.1921-4.28330.287112470.2366619846323195
4.2833-4.38280.294313170.2305637646508198
4.3828-4.49240.294713030.229637746507797
4.4924-4.61380.261713090.2166637096501898
4.6138-4.74940.282713100.2136638876519798
4.7494-4.90260.277412910.2127638166510797
4.9026-5.07770.261513200.2036643686568899
5.0777-5.28070.250213060.1942642386554498
5.2807-5.52080.264113080.1993641056541398
5.5208-5.81140.265612680.2029627786404696
5.8114-6.17490.260713250.2006647166604199
6.1749-6.65070.260313370.21016543566772100
6.6507-7.31810.274813360.21396544966785100
7.3181-8.37280.252313340.20666542066754100
8.3728-10.53260.252913370.21036535266689100
10.5326-49.99830.25312900.2308640316532198

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