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- PDB-4v8y: Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic T... -

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Basic information

Entry
Database: PDB / ID: 4v8y
TitleCryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex
Components
  • (40S RIBOSOMAL PROTEIN ...) x 31
  • (60S ACIDIC RIBOSOMAL PROTEIN ...) x 3
  • (60S RIBOSOMAL PROTEIN ...) x 40
  • (EUKARYOTIC RIBOSOMAL ...) x 2
  • 18S RIBOSOMAL RNA
  • 25S RIBOSOMAL RNA
  • 5.8S RIBOSOMAL RNA
  • 50S RIBOSOMAL PROTEIN L1
  • 5S RIBOSOMAL RNA
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 5B
  • GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN
  • SUPPRESSOR PROTEIN STM1
  • UBIQUITIN-40S RIBOSOMAL PROTEIN S31
  • UBIQUITIN-60S RIBOSOMAL PROTEIN L40
KeywordsRIBOSOME / RIBOSOME INITIATION COMPLEX / INITIATOR FACTOR EIF5B / SINGLE PARTICLE ANALYSIS
Function / homology
Function and homology information


triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / formation of cytoplasmic translation initiation complex / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / eukaryotic 48S preinitiation complex / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / formation of cytoplasmic translation initiation complex / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / eukaryotic 48S preinitiation complex / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / protein-synthesizing GTPase / ribosome-associated ubiquitin-dependent protein catabolic process / regulation of translational initiation / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / 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 / telomeric DNA binding / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / TOR signaling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / positive regulation of protein kinase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / 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 / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / regulation of translational fidelity / protein-RNA complex assembly / translational termination / ribosomal subunit export from nucleus / 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) / ribosomal small subunit export from nucleus / translation regulator activity / translation initiation factor binding / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / translation initiation factor activity / rescue of stalled ribosome / telomere maintenance / protein kinase C binding / cellular response to amino acid starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA / small-subunit processome / translational initiation / 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 / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / 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 / GTPase activity
Similarity search - Function
Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily ...Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 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 S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / 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 L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / S27a-like superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e / Ribosomal protein L6e signature. / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Plectin/S10 domain / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / : / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S7e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L34e, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L34e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein S3Ae, conserved site / Ribosomal protein L36e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / osmium (III) hexammine / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / 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 eL20B / 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 uL2B / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL29B / Small ribosomal subunit protein eS32B / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / 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 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein eL14B / Suppressor protein STM1 / Eukaryotic translation initiation factor 5B / Small ribosomal subunit protein eS26A / 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 / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsFernandez, I.S. / Bai, X.C. / Hussain, T. / Kelley, A.C. / Lorsch, J.R. / Ramakrishnan, V. / Scheres, S.H.W.
CitationJournal: Science / Year: 2013
Title: Molecular architecture of a eukaryotic translational initiation complex.
Authors: Israel S Fernández / Xiao-Chen Bai / Tanweer Hussain / Ann C Kelley / Jon R Lorsch / V Ramakrishnan / Sjors H W Scheres /
Abstract: The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start ...The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes.
History
DepositionJul 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4BYL, 4BYN, 4BYO, 4BYP, 4BYQ, 4BYR, 4BYS
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 22, 2015Group: Other
Revision 2.0Aug 2, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / em_software ...atom_site / em_software / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
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_atom_id / _atom_site.label_atom_id / _em_software.image_processing_id / _em_software.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2
Revision 3.0Apr 18, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_database_status / pdbx_entity_src_syn / struct_ref_seq
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.process_site / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 4.0Jun 19, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_sheet
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _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.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.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_type.id / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 5.0Jun 26, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_validate_torsion / struct_conn / struct_mon_prot_cis
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.label_comp_id / _pdbx_validate_torsion.auth_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_mon_prot_cis.auth_comp_id / _struct_mon_prot_cis.label_comp_id
Revision 5.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Assembly

Deposited unit
A0: 40S RIBOSOMAL PROTEIN S26-A
A1: 40S RIBOSOMAL PROTEIN S27-A
A2: 40S RIBOSOMAL PROTEIN S28-A
A3: 40S RIBOSOMAL PROTEIN S29-A
A4: 40S RIBOSOMAL PROTEIN S30-A
A5: UBIQUITIN-40S RIBOSOMAL PROTEIN S31
A6: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN
A7: SUPPRESSOR PROTEIN STM1
AA: 40S RIBOSOMAL PROTEIN S0-A
AB: 40S RIBOSOMAL PROTEIN S1-A
AC: 40S RIBOSOMAL PROTEIN S2
AD: 40S RIBOSOMAL PROTEIN S3
AE: 40S RIBOSOMAL PROTEIN S4-A
AF: 40S RIBOSOMAL PROTEIN S5
AG: 40S RIBOSOMAL PROTEIN S6-A
AH: 40S RIBOSOMAL PROTEIN S7-A
AI: 40S RIBOSOMAL PROTEIN S8-A
AJ: 40S RIBOSOMAL PROTEIN S9-A
AK: 40S RIBOSOMAL PROTEIN S10-A
AL: 40S RIBOSOMAL PROTEIN S11-A
AM: 40S RIBOSOMAL PROTEIN S12
AN: 40S RIBOSOMAL PROTEIN S13
AO: 40S RIBOSOMAL PROTEIN S14-A
AP: 40S RIBOSOMAL PROTEIN S15
AQ: 40S RIBOSOMAL PROTEIN S16-A
AR: 40S RIBOSOMAL PROTEIN S17-A
AS: 40S RIBOSOMAL PROTEIN S18-A
AT: 40S RIBOSOMAL PROTEIN S19-A
AU: 40S RIBOSOMAL PROTEIN S20
AV: 40S RIBOSOMAL PROTEIN S21-A
AW: 40S RIBOSOMAL PROTEIN S22-A
AX: 40S RIBOSOMAL PROTEIN S23-A
AY: 40S RIBOSOMAL PROTEIN S24-A
AZ: 40S RIBOSOMAL PROTEIN S25-A
BA: 60S RIBOSOMAL PROTEIN L2-B
BB: 60S RIBOSOMAL PROTEIN L3
BC: 60S RIBOSOMAL PROTEIN L4-A
BD: 60S RIBOSOMAL PROTEIN L5
BE: 60S RIBOSOMAL PROTEIN L6-A
BF: 60S RIBOSOMAL PROTEIN L7-A
BG: 60S RIBOSOMAL PROTEIN L8-A
BH: 60S RIBOSOMAL PROTEIN L9-A
BI: 60S RIBOSOMAL PROTEIN L10
BJ: 60S RIBOSOMAL PROTEIN L11-A
BK: 60S RIBOSOMAL PROTEIN L11-A
BL: 60S RIBOSOMAL PROTEIN L13-A
BM: 60S RIBOSOMAL PROTEIN L14-B
BN: 60S RIBOSOMAL PROTEIN L15-A
BO: 60S RIBOSOMAL PROTEIN L16-A
BP: 60S RIBOSOMAL PROTEIN L17-A
BQ: 60S RIBOSOMAL PROTEIN L18-A
BR: 60S RIBOSOMAL PROTEIN L19-B
BS: 60S RIBOSOMAL PROTEIN L20-B
BT: 60S RIBOSOMAL PROTEIN L21-A
BU: 60S RIBOSOMAL PROTEIN L22-A
BV: 60S RIBOSOMAL PROTEIN L23-A
BW: 60S RIBOSOMAL PROTEIN L24-A
BX: 60S RIBOSOMAL PROTEIN L25
BY: 60S RIBOSOMAL PROTEIN L26-A
BZ: 60S RIBOSOMAL PROTEIN L27-A
Ba: 60S RIBOSOMAL PROTEIN L28
Bb: 60S RIBOSOMAL PROTEIN L29
Bc: 60S RIBOSOMAL PROTEIN L30
Bd: 60S RIBOSOMAL PROTEIN L31-A
Be: 60S RIBOSOMAL PROTEIN L32
Bf: 60S RIBOSOMAL PROTEIN L33-A
Bg: 60S RIBOSOMAL PROTEIN L34-A
Bh: 60S RIBOSOMAL PROTEIN L35-B
Bi: 60S RIBOSOMAL PROTEIN L36-A
Bj: 60S RIBOSOMAL PROTEIN L37-A
Bk: 60S RIBOSOMAL PROTEIN L38
Bl: 60S RIBOSOMAL PROTEIN L39
Bm: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
Bn: 60S RIBOSOMAL PROTEIN L41-B
Bo: 60S RIBOSOMAL PROTEIN L42-A
Bq: 60S ACIDIC RIBOSOMAL PROTEIN P0
Br: 60S ACIDIC RIBOSOMAL PROTEIN P1
Bs: 60S ACIDIC RIBOSOMAL PROTEIN P2
By: 50S RIBOSOMAL PROTEIN L1
B2: 18S RIBOSOMAL RNA
B5: 25S RIBOSOMAL RNA
B7: 5S RIBOSOMAL RNA
B8: 5.8S RIBOSOMAL RNA
CL: 50S RIBOSOMAL PROTEIN L1
CN: EUKARYOTIC RIBOSOMAL L1_RRNA
CP: EUKARYOTIC TRANSLATION INITIATION FACTOR 5B
CW: EUKARYOTIC RIBOSOMAL P_E TRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,376,539482
Polymers3,314,56987
Non-polymers61,970395
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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40S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules A0A1A2A3A4AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZ

#1: Protein 40S RIBOSOMAL PROTEIN S26-A


Mass: 13538.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39938
#2: Protein 40S RIBOSOMAL PROTEIN S27-A / RP61 / YS20


Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P35997
#3: Protein 40S RIBOSOMAL PROTEIN S28-A / S33 / YS27


Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q3E7X9
#4: Protein 40S RIBOSOMAL PROTEIN S29-A / S36 / YS29


Mass: 6675.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P41057
#5: Protein 40S RIBOSOMAL PROTEIN S30-A


Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX33
#9: Protein 40S RIBOSOMAL PROTEIN S0-A / NUCLEIC ACID-BINDING PROTEIN NAB1A


Mass: 28051.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32905
#10: Protein 40S RIBOSOMAL PROTEIN S1-A / RP10A


Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P33442
#11: Protein 40S RIBOSOMAL PROTEIN S2 / OMNIPOTENT SUPPRESSOR PROTEIN SUP44 / RP12 / S4 / YS5


Mass: 27490.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P25443
#12: Protein 40S RIBOSOMAL PROTEIN S3 / RP13 / YS3


Mass: 26542.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05750
#13: Protein 40S RIBOSOMAL PROTEIN S4-A / RP5 / S7 / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX35
#14: Protein 40S RIBOSOMAL PROTEIN S5 / RP14 / S2 / YS8


Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P26783
#15: Protein 40S RIBOSOMAL PROTEIN S6-A / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX37
#16: Protein 40S RIBOSOMAL PROTEIN S7-A / RP30 / RP40


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P26786
#17: Protein 40S RIBOSOMAL PROTEIN S8-A / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX39
#18: Protein 40S RIBOSOMAL PROTEIN S9-A / RP21 / S13 / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: O13516
#19: Protein 40S RIBOSOMAL PROTEIN S10-A


Mass: 12757.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q08745
#20: Protein 40S RIBOSOMAL PROTEIN S11-A / RP41 / S18 / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX47
#21: Protein 40S RIBOSOMAL PROTEIN S12


Mass: 15488.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P48589
#22: Protein 40S RIBOSOMAL PROTEIN S13 / S27A / YS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05756
#23: Protein 40S RIBOSOMAL PROTEIN S14-A / RP59A


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P06367
#24: Protein 40S RIBOSOMAL PROTEIN S15 / RIG PROTEIN / RP52 / S21 / YS21


Mass: 16031.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q01855
#25: Protein 40S RIBOSOMAL PROTEIN S16-A / RP61R


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX51
#26: Protein 40S RIBOSOMAL PROTEIN S17-A / RP51A


Mass: 15820.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P02407
#27: Protein 40S RIBOSOMAL PROTEIN S18-A


Mass: 17071.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX55
#28: Protein 40S RIBOSOMAL PROTEIN S19-A / RP55A / S16A / YP45 / YS16A


Mass: 15942.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P07280
#29: Protein 40S RIBOSOMAL PROTEIN S20


Mass: 13929.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38701
#30: Protein 40S RIBOSOMAL PROTEIN S21-A / S26 / YS25


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0C0V8
#31: Protein 40S RIBOSOMAL PROTEIN S22-A / RP50 / S24 / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0C0W1
#32: Protein 40S RIBOSOMAL PROTEIN S23-A / RP37 / S28 / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX29
#33: Protein 40S RIBOSOMAL PROTEIN S24-A / RP50


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX31
#34: Protein 40S RIBOSOMAL PROTEIN S25-A / RP45 / S31 / YS23


Mass: 12067.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q3E792

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Protein , 6 types, 7 molecules A5A6A7BmByCLCP

#6: Protein UBIQUITIN-40S RIBOSOMAL PROTEIN S31 / CEP76 / S37 / YS24


Mass: 16559.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05759
#7: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN / RECEPTOR FOR ACTIVATED C KINASE / RECEPTOR OF ACTIVATED PROTEIN KINASE C 1 / RACK1


Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38011
#8: Protein 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: 29052.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39015
#73: Protein UBIQUITIN-60S RIBOSOMAL PROTEIN L40 / CEP52


Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CH08
#79: Protein 50S RIBOSOMAL PROTEIN L1


Mass: 24867.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#85: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 5B / EIF-5B / TRANSLATION INITIATION FACTOR IF-2 / INITIATION FACTOR EIF5B


Mass: 37861.547 Da / Num. of mol.: 1 / Fragment: DOMAIN 1 AND 2, RESIDUES 401-739 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39730

+
60S RIBOSOMAL PROTEIN ... , 40 types, 40 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBd...

#35: Protein 60S RIBOSOMAL PROTEIN L2-B / L5 / RP8 / YL6


Mass: 27332.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX46
#36: Protein 60S RIBOSOMAL PROTEIN L3 / MAINTENANCE OF KILLER PROTEIN 8 / RP1 / TRICHODERMIN RESISTANCE PROTEIN YL1


Mass: 43719.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P14126
#37: Protein 60S RIBOSOMAL PROTEIN L4-A / L2 / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P10664
#38: Protein 60S RIBOSOMAL PROTEIN L5 / L1 / L1A / RIBOSOMAL 5S RNA-BINDING PROTEIN / YL3


Mass: 33633.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P26321
#39: Protein 60S RIBOSOMAL PROTEIN L6-A / L17 / RP18 / YL16


Mass: 19869.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q02326
#40: Protein 60S RIBOSOMAL PROTEIN L7-A / L6 / RP11 / YL8


Mass: 27555.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05737
#41: 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.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P17076
#42: Protein 60S RIBOSOMAL PROTEIN L9-A / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05738
#43: Protein 60S RIBOSOMAL PROTEIN L10 / L9 / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX SUBUNIT VI-REQUIRING PROTEIN


Mass: 25279.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P41805
#44: Protein 60S RIBOSOMAL PROTEIN L11-A / L16 / RP39 / YL22


Mass: 19624.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0C0W9
#45: Protein 60S RIBOSOMAL PROTEIN L11-A


Mass: 14826.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#46: Protein 60S RIBOSOMAL PROTEIN L13-A


Mass: 22472.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q12690
#47: Protein 60S RIBOSOMAL PROTEIN L14-B


Mass: 15063.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38754
#48: Protein 60S RIBOSOMAL PROTEIN L15-A / L13 / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05748
#49: Protein 60S RIBOSOMAL PROTEIN L16-A / L13A / L21 / RP22 / YL15


Mass: 22116.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P26784
#50: Protein 60S RIBOSOMAL PROTEIN L17-A / L20A / YL17


Mass: 20458.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05740
#51: Protein 60S RIBOSOMAL PROTEIN L18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX49
#52: Protein 60S RIBOSOMAL PROTEIN L19-B / L23 / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX83
#53: Protein 60S RIBOSOMAL PROTEIN L20-B / L18A


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX24
#54: Protein 60S RIBOSOMAL PROTEIN L21-A


Mass: 18148.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q02753
#55: Protein 60S RIBOSOMAL PROTEIN L22-A / L1C / RP4 / YL31


Mass: 13580.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05749
#56: Protein 60S RIBOSOMAL PROTEIN L23-A / L17A / YL32


Mass: 14362.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX41
#57: Protein 60S RIBOSOMAL PROTEIN L24-A / L30 / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04449
#58: Protein 60S RIBOSOMAL PROTEIN L25 / RP16L / YL25 / "YP42"


Mass: 15656.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04456
#59: Protein 60S RIBOSOMAL PROTEIN L26-A / L33 / YL33


Mass: 14134.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05743
#60: Protein 60S RIBOSOMAL PROTEIN L27-A


Mass: 15437.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0C2H6
#61: Protein 60S RIBOSOMAL PROTEIN L28 / L27A / L29 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P02406
#62: Protein 60S RIBOSOMAL PROTEIN L29 / YL43


Mass: 6560.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05747
#63: Protein 60S RIBOSOMAL PROTEIN L30 / L32 / RP73 / YL38


Mass: 11299.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P14120
#64: Protein 60S RIBOSOMAL PROTEIN L31-A / L34 / YL28


Mass: 12848.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0C2H8
#65: Protein 60S RIBOSOMAL PROTEIN L32


Mass: 14678.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38061
#66: Protein 60S RIBOSOMAL PROTEIN L33-A / L37 / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05744
#67: Protein 60S RIBOSOMAL PROTEIN L34-A


Mass: 13542.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P87262
#68: Protein 60S RIBOSOMAL PROTEIN L35-B


Mass: 13811.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX85
#69: Protein 60S RIBOSOMAL PROTEIN L36-A / L39 / YL39


Mass: 11020.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05745
#70: Protein 60S RIBOSOMAL PROTEIN L37-A / L43 / YL35 / YP55


Mass: 9746.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P49166
#71: Protein 60S RIBOSOMAL PROTEIN L38


Mass: 8714.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P49167
#72: Protein/peptide 60S RIBOSOMAL PROTEIN L39 / L46 / YL40


Mass: 6227.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04650
#74: Protein/peptide 60S RIBOSOMAL PROTEIN L41-B / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX87
#75: Protein 60S RIBOSOMAL PROTEIN L42-A / L41 / YL27 / YP44


Mass: 12115.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CX27

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60S ACIDIC RIBOSOMAL PROTEIN ... , 3 types, 3 molecules BqBrBs

#76: Protein 60S ACIDIC RIBOSOMAL PROTEIN P0 / A0 / L10E


Mass: 33749.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05317
#77: Protein/peptide 60S ACIDIC RIBOSOMAL PROTEIN P1


Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#78: Protein/peptide 60S ACIDIC RIBOSOMAL PROTEIN P2


Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)

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RNA chain , 4 types, 4 molecules B2B5B7B8

#80: RNA chain 18S RIBOSOMAL RNA


Mass: 577937.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#81: RNA chain 25S RIBOSOMAL RNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: GenBank: BK006945
#82: RNA chain 5S RIBOSOMAL RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: GenBank: AE016820
#83: RNA chain 5.8S RIBOSOMAL RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: GenBank: HQ026735

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EUKARYOTIC RIBOSOMAL ... , 2 types, 2 molecules CNCW

#84: RNA chain EUKARYOTIC RIBOSOMAL L1_RRNA


Mass: 28286.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#86: RNA chain EUKARYOTIC RIBOSOMAL P_E TRNA


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast), (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)

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Non-polymers , 4 types, 395 molecules

#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#88: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 191 / Source method: obtained synthetically / Formula: Mg
#89: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 197 / Source method: obtained synthetically / Formula: H12N6Os
#90: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM

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Details

Has protein modificationN
Sequence detailsTHESE ARE PARTS OF THE PROTEIN SEQUENCES MODELED AS UNK RESIDUES.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 80S-EIF5B-MET-ITRNAMET EUKARYOTIC TRANSLATION INITIATION COMPLEX WITH TRNA IN THE PE-SITE AND ONLY DENSITY FOR THE G DOMAIN AND DOMAIN II
Type: RIBOSOME
Buffer solutionName: 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
pH: 7.2
Details: 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: FORMVAR PLUS CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Jan 15, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 79096 X / Nominal defocus max: 3900 nm / Nominal defocus min: 1900 nm / Cs: 2 mm
Specimen holderTemperature: 85 K
Image recordingElectron dose: 16 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)
Image scansNum. digital images: 1012
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2RELION3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Num. of particles: 40729 / Actual pixel size: 1.77 Å
Magnification calibration: CROSS-CORRELATION BETWEEN CRYO-EM MAP AND CRYSTAL STRUCTURE
Details: USE A NEWLY DEVELOPED STATISTICAL MOVIE PROCESSING APPROACH TO COMPENSATE FOR BEAM-INDUCED MOVEMENT. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2421. (DEPOSITION ID: 11807).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Details: METHOD--RIGID-BODY FITTING
RefinementHighest resolution: 4.3 Å
Refinement stepCycle: LAST / Highest resolution: 4.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39033 0 4 0 39037

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