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- PDB-5tga: Crystal structure of the S.cerevisiae 80S ribosome in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5tga
TitleCrystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro
Components
  • (18S ribosomal ...) x 2
  • (40S ribosomal protein ...) x 13
  • (60S Ribosomal Protein ...) x 35
  • (Large ribosomal subunit protein ...) x 9
  • (Small ribosomal subunit protein ...) x 20
  • (Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound protein ...) x 2
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Peptidyl-tRNA analog ACCA-Pro
  • Rps5p
KeywordsRIBOSOME / translation / protein synthesis / proline / aminoacyl-tRNA / peptide bond formation / catalysis / cyclic amino acids
Function / homology
Function and homology information


triplex DNA binding / Platelet degranulation / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / : ...triplex DNA binding / Platelet degranulation / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / 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 / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / telomeric DNA binding / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of protein kinase activity / TOR signaling / negative regulation of translational frameshifting / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / G-protein alpha-subunit binding / ribosomal large subunit export from nucleus / 90S preribosome / Ub-specific processing proteases / translational termination / regulation of translational fidelity / ribosomal subunit export from nucleus / protein-RNA complex assembly / maturation of LSU-rRNA / 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) / translation repressor activity / translation regulator activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled cytosolic ribosome / telomere maintenance / cellular response to amino acid starvation / protein kinase C binding / ribosome assembly / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / macroautophagy / maturation of SSU-rRNA / translational initiation / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / mitochondrion / DNA binding
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 / : / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain ...Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S12e / Ribosomal protein L27e, conserved site / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / 40S Ribosomal protein S10 / Ribosomal protein L19e signature. / Ribosomal protein L24e, conserved site / : / Ribosomal protein L24e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L6e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal L40e family / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S30 / : / Ribosomal protein S30 / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S7e signature. / Ribosomal protein S25 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / S25 ribosomal protein / Ribosomal protein L30e signature 1. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L27e
Similarity search - Domain/homology
osmium (III) hexammine / PROLINE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...osmium (III) hexammine / PROLINE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Rps5p / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / 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 eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / 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 / Small ribosomal subunit protein eS32B / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS17B / 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 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 uS11B / 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 / Large ribosomal subunit protein eL13A / Large ribosomal subunit protein uL5B / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsMelnikov, S. / Mailliot, J.
CitationJournal: EMBO Rep. / Year: 2016
Title: Molecular insights into protein synthesis with proline residues.
Authors: Melnikov, S. / Mailliot, J. / Rigger, L. / Neuner, S. / Shin, B.S. / Yusupova, G. / Dever, T.E. / Micura, R. / Yusupov, M.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_conn_type.id
Revision 2.0Dec 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_ref / struct_ref_seq
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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _entity_src_nat.common_name / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: 18S ribosomal RNA
S0: 40S ribosomal protein S0-A
S1: Small ribosomal subunit protein eS1A
S2: Small ribosomal subunit protein uS5
S3: Small ribosomal subunit protein uS3
S4: Small ribosomal subunit protein eS4A
S5: Rps5p
S6: Small ribosomal subunit protein eS6A
S7: Small ribosomal subunit protein eS7A
S8: Small ribosomal subunit protein eS8A
S9: Small ribosomal subunit protein uS4A
C0: Small ribosomal subunit protein eS10A
C1: Small ribosomal subunit protein uS17A
C2: Small ribosomal subunit protein eS12
C3: 40S ribosomal protein S13
C4: Small ribosomal subunit protein uS11B
C5: Small ribosomal subunit protein uS19
C6: Small ribosomal subunit protein uS9A
C7: 40S ribosomal protein S17-A
C8: 40S ribosomal protein S18-A
C9: 40S ribosomal protein S19-A
D0: Small ribosomal subunit protein uS10
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: Small ribosomal subunit protein eS25A
D6: 40S ribosomal protein S26-B
D7: 40S ribosomal protein S27-A
D8: 40S ribosomal protein S28-A
D9: 40S ribosomal protein S29-A
E0: Small ribosomal subunit protein eS30A
E1: Small ribosomal subunit protein eS31
SR: Small ribosomal subunit protein RACK1
SM: Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound 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: Large ribosomal subunit protein eL6A
L7: Large ribosomal subunit protein uL30A
L8: 60S ribosomal protein L8-A
L9: 60S ribosomal protein L9-A
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11-B
M3: Large ribosomal subunit protein eL13A
M4: Large ribosomal subunit protein eL14A
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: Large ribosomal subunit protein eL24A
N5: 60S ribosomal protein L25
N6: Large ribosomal subunit protein uL24A
N7: 60S ribosomal protein L27-A
N8: 60S ribosomal protein L28
N9: 60S ribosomal protein L29
O0: Large ribosomal subunit protein eL30
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: 60S ribosomal protein L40-A
Q1: Large ribosomal subunit protein eL41B
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
6: 18S ribosomal RNA
s0: 40S ribosomal protein S0-A
s1: Small ribosomal subunit protein eS1A
s2: Small ribosomal subunit protein uS5
s3: Small ribosomal subunit protein uS3
s4: Small ribosomal subunit protein eS4A
s5: Rps5p
s6: Small ribosomal subunit protein eS6A
s7: Small ribosomal subunit protein eS7A
s8: Small ribosomal subunit protein eS8A
s9: Small ribosomal subunit protein uS4A
c0: Small ribosomal subunit protein eS10A,40S ribosomal protein S10-A,40S ribosomal protein S10-A,40S Ribosomal Protein S10-A
c1: Small ribosomal subunit protein uS17A
c2: Small ribosomal subunit protein eS12
c3: 40S ribosomal protein S13
c4: Small ribosomal subunit protein uS11B
c5: Small ribosomal subunit protein uS19
c6: Small ribosomal subunit protein uS9A
c7: 40S ribosomal protein S17-A
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: Small ribosomal subunit protein uS10
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: Small ribosomal subunit protein eS25A
d6: 40S ribosomal protein S26-B
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
e0: Small ribosomal subunit protein eS30A
e1: Small ribosomal subunit protein eS31
sR: Small ribosomal subunit protein RACK1
sM: Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound 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: Large ribosomal subunit protein eL6A
l7: Large ribosomal subunit protein uL30A
l8: 60S ribosomal protein L8-A
l9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-B
m2: 60S Ribosomal Protein L12
m3: Large ribosomal subunit protein eL13A
m4: Large ribosomal subunit protein eL14A
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: Large ribosomal subunit protein eL24A
n5: 60S ribosomal protein L25
n6: Large ribosomal subunit protein uL24A
n7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
o0: Large ribosomal subunit protein eL30
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: 60S ribosomal protein L40-A
q1: Large ribosomal subunit protein eL41B
q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
p0: Large ribosomal subunit protein uL10
p1: 60S Ribosomal Protein P1/2
p2: 60S Ribosomal Protein P1/2
A: Peptidyl-tRNA analog ACCA-Pro
B: Peptidyl-tRNA analog ACCA-Pro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,585,8803719
Polymers6,146,166164
Non-polymers439,7143555
Water00
1
2: 18S ribosomal RNA
S0: 40S ribosomal protein S0-A
S1: Small ribosomal subunit protein eS1A
S2: Small ribosomal subunit protein uS5
S3: Small ribosomal subunit protein uS3
S4: Small ribosomal subunit protein eS4A
S5: Rps5p
S6: Small ribosomal subunit protein eS6A
S7: Small ribosomal subunit protein eS7A
S8: Small ribosomal subunit protein eS8A
S9: Small ribosomal subunit protein uS4A
C0: Small ribosomal subunit protein eS10A
C1: Small ribosomal subunit protein uS17A
C2: Small ribosomal subunit protein eS12
C3: 40S ribosomal protein S13
C4: Small ribosomal subunit protein uS11B
C5: Small ribosomal subunit protein uS19
C6: Small ribosomal subunit protein uS9A
C7: 40S ribosomal protein S17-A
C8: 40S ribosomal protein S18-A
C9: 40S ribosomal protein S19-A
D0: Small ribosomal subunit protein uS10
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: Small ribosomal subunit protein eS25A
D6: 40S ribosomal protein S26-B
D7: 40S ribosomal protein S27-A
D8: 40S ribosomal protein S28-A
D9: 40S ribosomal protein S29-A
E0: Small ribosomal subunit protein eS30A
E1: Small ribosomal subunit protein eS31
SR: Small ribosomal subunit protein RACK1
SM: Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound 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: Large ribosomal subunit protein eL6A
L7: Large ribosomal subunit protein uL30A
L8: 60S ribosomal protein L8-A
L9: 60S ribosomal protein L9-A
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11-B
M3: Large ribosomal subunit protein eL13A
M4: Large ribosomal subunit protein eL14A
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: Large ribosomal subunit protein eL24A
N5: 60S ribosomal protein L25
N6: Large ribosomal subunit protein uL24A
N7: 60S ribosomal protein L27-A
N8: 60S ribosomal protein L28
N9: 60S ribosomal protein L29
O0: Large ribosomal subunit protein eL30
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: 60S ribosomal protein L40-A
Q1: Large ribosomal subunit protein eL41B
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
A: Peptidyl-tRNA analog ACCA-Pro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,272,9431774
Polymers3,058,65380
Non-polymers214,2901694
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
6: 18S ribosomal RNA
s0: 40S ribosomal protein S0-A
s1: Small ribosomal subunit protein eS1A
s2: Small ribosomal subunit protein uS5
s3: Small ribosomal subunit protein uS3
s4: Small ribosomal subunit protein eS4A
s5: Rps5p
s6: Small ribosomal subunit protein eS6A
s7: Small ribosomal subunit protein eS7A
s8: Small ribosomal subunit protein eS8A
s9: Small ribosomal subunit protein uS4A
c0: Small ribosomal subunit protein eS10A,40S ribosomal protein S10-A,40S ribosomal protein S10-A,40S Ribosomal Protein S10-A
c1: Small ribosomal subunit protein uS17A
c2: Small ribosomal subunit protein eS12
c3: 40S ribosomal protein S13
c4: Small ribosomal subunit protein uS11B
c5: Small ribosomal subunit protein uS19
c6: Small ribosomal subunit protein uS9A
c7: 40S ribosomal protein S17-A
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: Small ribosomal subunit protein uS10
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: Small ribosomal subunit protein eS25A
d6: 40S ribosomal protein S26-B
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
e0: Small ribosomal subunit protein eS30A
e1: Small ribosomal subunit protein eS31
sR: Small ribosomal subunit protein RACK1
sM: Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound 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: Large ribosomal subunit protein eL6A
l7: Large ribosomal subunit protein uL30A
l8: 60S ribosomal protein L8-A
l9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-B
m2: 60S Ribosomal Protein L12
m3: Large ribosomal subunit protein eL13A
m4: Large ribosomal subunit protein eL14A
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: Large ribosomal subunit protein eL24A
n5: 60S ribosomal protein L25
n6: Large ribosomal subunit protein uL24A
n7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
o0: Large ribosomal subunit protein eL30
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: 60S ribosomal protein L40-A
q1: Large ribosomal subunit protein eL41B
q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
p0: Large ribosomal subunit protein uL10
p1: 60S Ribosomal Protein P1/2
p2: 60S Ribosomal Protein P1/2
B: Peptidyl-tRNA analog ACCA-Pro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,312,9371945
Polymers3,087,51384
Non-polymers225,4241861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)435.450, 288.140, 304.160
Angle α, β, γ (deg.)90.000, 99.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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18S ribosomal ... , 2 types, 2 molecules 26

#1: RNA chain 18S ribosomal RNA


Mass: 589169.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1262303
#80: RNA chain 18S ribosomal RNA


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 768837330

-
40S ribosomal protein ... , 13 types, 26 molecules S0s0C3c3C7c7C8c8C9c9D1d1D2d2D3d3D4d4D6d6D7d7D8d8D9d9

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


Mass: 22811.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B3LI22
#15: Protein 40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 16928.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756
#19: Protein 40S ribosomal protein S17-A / RP51A / Small ribosomal subunit protein eS17-A


Mass: 14268.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02407, UniProt: P14127*PLUS
#20: Protein 40S ribosomal protein S18-A / Small ribosomal subunit protein uS13-A


Mass: 16940.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX55
#21: Protein 40S ribosomal protein S19-A / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07280
#23: Protein 40S ribosomal protein S21-A / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0V8
#24: Protein 40S ribosomal protein S22-A / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W1
#25: Protein 40S ribosomal protein S23-A / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 15942.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX29
#26: Protein 40S ribosomal protein S24-A / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15231.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX31
#28: Protein 40S ribosomal protein S26-B / Small ribosomal subunit protein eS26-B


Mass: 11022.989 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39939
#29: Protein 40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8762.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35997
#30: Protein 40S ribosomal protein S28-A / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7116.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7X9
#31: Protein 40S ribosomal protein S29-A / S36 / Small ribosomal subunit protein uS14-A / YS29


Mass: 6335.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41057

-
Small ribosomal subunit protein ... , 20 types, 38 molecules S1s1S2s2S3s3S4s4S6s6S7s7S8s8S9s9C0C1c1C2c2C4c4C5c5C6c6D0d0D5...

#3: Protein Small ribosomal subunit protein eS1A / 40S ribosomal protein S1-A / RP10A


Mass: 24498.365 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33442, UniProt: B3RHV0*PLUS
#4: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


Mass: 23212.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443
#5: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3 / RP13 / YS3


Mass: 24702.791 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05750
#6: Protein Small ribosomal subunit protein eS4A


Mass: 29338.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX35
#8: Protein Small ribosomal subunit protein eS6A


Mass: 25895.072 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX37
#9: Protein Small ribosomal subunit protein eS7A / 40S ribosomal protein S7-A / RP30 / RP40


Mass: 21158.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26786
#10: Protein Small ribosomal subunit protein eS8A / 40S ribosomal protein S8-A / RP19 / S14 / YS9


Mass: 22406.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX39
#11: Protein Small ribosomal subunit protein uS4A


Mass: 21210.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516
#12: Protein Small ribosomal subunit protein eS10A / 40S ribosomal protein S10-A


Mass: 11571.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08745
#13: Protein Small ribosomal subunit protein uS17A / 40S ribosomal protein S11-A / RP41 / S18 / YS12


Mass: 17654.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX47
#14: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 13327.331 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48589
#16: Protein Small ribosomal subunit protein uS11B / 40S ribosomal protein S14-B / RP59B


Mass: 13560.528 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39516
#17: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein / RP52 / S21 / YS21


Mass: 15232.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01855
#18: Protein Small ribosomal subunit protein uS9A / 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 (brewer's yeast) / References: UniProt: P0CX51
#22: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 12575.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38701
#27: Protein Small ribosomal subunit protein eS25A / 40S ribosomal protein S25-A / RP45 / S31 / YS23


Mass: 8001.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E792
#32: Protein Small ribosomal subunit protein eS30A / 40S ribosomal protein S30-A


Mass: 7006.346 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX33
#33: Protein Small ribosomal subunit protein eS31 / 40S ribosomal protein S31 / CEP76 / S37 / YS24


Mass: 8703.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05759
#34: Protein Small ribosomal subunit protein RACK1


Mass: 34710.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38011
#81: Protein Small ribosomal subunit protein eS10A,40S ribosomal protein S10-A,40S ribosomal protein S10-A,40S Ribosomal Protein S10-A / 40S ribosomal protein S10-A


Mass: 11181.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08745

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Protein , 1 types, 2 molecules S5s5

#7: Protein Rps5p


Mass: 22908.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A1L4AA68, UniProt: P26783*PLUS

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Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound protein ... , 2 types, 2 molecules SMsM

#35: Protein Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound 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: 16519.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39015
#82: Protein Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound 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: 10310.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39015

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RNA chain , 4 types, 8 molecules 153748AB

#36: RNA chain 25S ribosomal RNA


Mass: 1096842.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822
#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 (brewer's yeast) / References: GenBank: 1039024011
#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 (brewer's yeast) / References: GenBank: 1331532632
#86: RNA chain Peptidyl-tRNA analog ACCA-Pro


Mass: 893.627 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

+
60S Ribosomal Protein ... , 35 types, 69 molecules L2l2L3l3L4l4L5l5L8l8L9l9M0m0M1m1M5m5M6m6M7m7M8m8M9m9N0n0N1n1...

#39: Protein 60S ribosomal protein L2-A / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27217.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX45
#40: Protein 60S ribosomal protein L3 / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43719.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#41: Protein 60S ribosomal protein L4-A / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664
#42: Protein 60S ribosomal protein L5 / L1 / L1a / Large ribosomal subunit protein uL18 / 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 (brewer's yeast) / References: UniProt: P26321
#45: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25814.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076
#46: Protein 60S ribosomal protein L9-A / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05738
#47: Protein 60S ribosomal protein L10 / L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI- ...L9 / Large ribosomal subunit protein uL16 / 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 (brewer's yeast) / References: UniProt: P41805
#48: Protein 60S ribosomal protein L11-B / L16 / Large ribosomal subunit protein uL5-B / RP39 / YL22


Mass: 19266.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E757
#51: Protein 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748
#52: Protein 60S ribosomal protein L16-A / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#53: Protein 60S ribosomal protein L17-A / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20458.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740
#54: Protein 60S ribosomal protein L18-A / Large ribosomal subunit protein eL18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX49
#55: Protein 60S ribosomal protein L19-A / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX82
#56: Protein 60S ribosomal protein L20-A / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX23
#57: Protein 60S ribosomal protein L21-A / Large ribosomal subunit protein eL21-A


Mass: 18148.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753
#58: Protein 60S ribosomal protein L22-A / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 11263.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05749
#59: Protein 60S ribosomal protein L23-A / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14362.755 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX41
#61: Protein 60S ribosomal protein L25 / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 13771.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456
#63: Protein 60S ribosomal protein L27-A / Large ribosomal subunit protein eL27-A


Mass: 15437.166 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H6
#64: Protein 60S ribosomal protein L28 / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406
#65: Protein 60S ribosomal protein L29 / Large ribosomal subunit protein eL29 / YL43


Mass: 6560.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05747
#67: Protein 60S ribosomal protein L31-A / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12649.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H8
#68: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 14478.054 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061
#69: Protein 60S ribosomal protein L33-A / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05744
#70: Protein 60S ribosomal protein L34-A / Large ribosomal subunit protein eL34-A


Mass: 12608.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P87262
#71: Protein 60S ribosomal protein L35-A / Large ribosomal subunit protein uL29-A


Mass: 13811.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX84
#72: Protein 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11020.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05745
#73: Protein 60S ribosomal protein L37-A / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9746.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166
#74: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8714.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49167
#75: Protein/peptide 60S ribosomal protein L39 / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6227.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650
#76: Protein 60S ribosomal protein L40-A / CEP52 / Large ribosomal subunit protein eL40-A


Mass: 6032.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08
#78: Protein 60S ribosomal protein L42-A / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 12115.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX27
#79: Protein 60S ribosomal protein L43-A / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 9981.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX25
#83: Protein 60S Ribosomal Protein L12


Mass: 12783.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#85: Protein/peptide 60S Ribosomal Protein P1/2


Mass: 4017.944 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

-
Large ribosomal subunit protein ... , 9 types, 17 molecules L6l6L7l7M3m3M4m4N4n4N6n6O0o0Q1q1p0

#43: Protein Large ribosomal subunit protein eL6A / 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 (brewer's yeast) / References: UniProt: Q02326
#44: Protein Large ribosomal subunit protein uL30A / 60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 25341.480 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#49: Protein Large ribosomal subunit protein eL13A / 60S ribosomal protein L13-A


Mass: 21956.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12690
#50: Protein Large ribosomal subunit protein eL14A / 60S ribosomal protein L14-A


Mass: 15063.870 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36105
#60: Protein Large ribosomal subunit protein eL24A / 60S ribosomal protein L24-A / L30 / RP29 / YL21


Mass: 15506.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04449
#62: Protein Large ribosomal subunit protein uL24A


Mass: 14134.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#66: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 10902.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120
#77: Protein/peptide Large ribosomal subunit protein eL41B / 60S ribosomal protein L41-B / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX87, UniProt: P0CX86*PLUS
#84: Protein Large ribosomal subunit protein uL10 / 60S acidic ribosomal protein P0 / A0 / L10e


Mass: 24044.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317

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Non-polymers , 4 types, 3555 molecules

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


Mass: 286.365 Da / Num. of mol.: 1345 / Source method: obtained synthetically / Formula: H12N6Os
#88: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2192 / Source method: obtained synthetically / Formula: Mg
#89: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#90: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2

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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: 3.17 Å3/Da / Density % sol: 61.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG20000

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→200 Å / Num. obs: 1026480 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 82.52 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.333 / Net I/σ(I): 6.51
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
3.3-3.41.4850.970.319191.7
3.4-3.51.1261.290.414192.9
3.5-3.60.891.630.525192.6
3.6-3.70.7361.970.617192.2
3.7-40.4792.960.778191.8
4-50.2255.930.941190.7
5-60.1259.970.981189.2
6-70.70310.840.912199.9
7-80.4814.140.9511100
8-90.36516.290.9681100
9-100.27819.420.9821100
10-250.16424.650.993199.9
25-500.05441.630.998199.8
50-1000.07232.590.993196.4
100-1250.04714.531127.3
1250.3118.90.952137

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
PHENIX1.10.1_2155phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→149.313 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.95
RfactorNum. reflection% reflection
Rfree0.2649 20446 2 %
Rwork0.2115 --
obs0.2125 1022264 92.31 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 231.38 Å2 / Biso mean: 73.4994 Å2 / Biso min: 21.63 Å2
Refinement stepCycle: final / Resolution: 3.3→149.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms179692 222781 11611 0 414084
Biso mean--67.43 --
Num. residues----33345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011440892
X-RAY DIFFRACTIONf_angle_d1.668654793
X-RAY DIFFRACTIONf_chiral_restr0.06879613
X-RAY DIFFRACTIONf_plane_restr0.00841819
X-RAY DIFFRACTIONf_dihedral_angle_d19.428237969
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 (%)
3.3-3.33750.35596280.313307523138085
3.3375-3.37680.3486540.3021320643271889
3.3768-3.4180.34546740.2963329833365792
3.418-3.46120.33976810.284334123409393
3.4612-3.50680.33116820.2835334463412892
3.5068-3.55480.34046800.2829332903397092
3.5548-3.60560.32516800.2824333153399592
3.6056-3.65940.33046780.2758332373391592
3.6594-3.71660.31646800.2612332813396192
3.7166-3.77750.32286780.2531332583393692
3.7775-3.84270.29856790.2372332733395292
3.8427-3.91260.29996740.2288330163369092
3.9126-3.98780.25756750.219330413371691
3.9878-4.06920.28036700.2186328553352591
4.0692-4.15770.26446590.2132322893294889
4.1577-4.25440.27236700.2079328353350591
4.2544-4.36080.2626750.1952330463372191
4.3608-4.47880.25276720.1892329473361991
4.4788-4.61060.23976700.1831328303350091
4.6106-4.75940.23656690.1792328113348091
4.7594-4.92950.24436670.175326343330190
4.9295-5.12690.23636650.1743326233328890
5.1269-5.36020.23056610.1599323813304289
5.3602-5.64280.20476520.1578319593261188
5.6428-5.99640.2216620.1658324083307089
5.9964-6.45940.24997390.17993619936938100
6.4594-7.10940.24497390.18013627837017100
7.1094-8.13810.22857420.18253630037042100
8.1381-10.25280.24847430.20233643337176100
10.2528-149.46550.25557480.2415366223737099

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