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- PDB-6gz3: tRNA translocation by the eukaryotic 80S ribosome and the impact ... -

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Basic information

Entry
Database: PDB / ID: 6gz3
TitletRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)
Components
  • (40S ribosomal protein ...) x 4
  • (Ribosomal protein ...) x 72
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S ribosomal protein L27
  • Ribosomal protein
  • ap/P-site tRNA
  • eukaryotic elongation factor 2 (eEF2)
  • mRNA
  • pe/E-site-tRNA
KeywordsRIBOSOME / translocation rabbit ribosome / 80S / eEF2 / head swivel / rotation
Function / homology
Function and homology information


ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / rough endoplasmic reticulum / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / maturation of SSU-rRNA ...ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / rough endoplasmic reticulum / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / maturation of SSU-rRNA / small-subunit processome / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / large ribosomal subunit / regulation of translation / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / apoptotic process / dendrite / synapse / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / RNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 ...Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / S27a-like superfamily / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Plectin/S10 domain / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / : / Ribosomal protein S7e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L37e, conserved site / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L37e signature.
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS12 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesEnterobacteria phage SP6 (virus)
Oryctolagus cuniculus (rabbit)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFlis, J. / Holm, M. / Rundlet, E.J. / Loerke, J. / Hilal, T. / Dabrowski, M. / Buerger, J. / Mielke, T. / Blanchard, S.C. / Spahn, C.M.T. / Budkevich, T.V.
Funding support Germany, United States, 3items
OrganizationGrant numberCountry
German Research FoundationDFG SFB 740 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079238 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM115327-Tan United States
CitationJournal: Cell Rep / Year: 2018
Title: tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.
Authors: Julia Flis / Mikael Holm / Emily J Rundlet / Justus Loerke / Tarek Hilal / Marylena Dabrowski / Jörg Bürger / Thorsten Mielke / Scott C Blanchard / Christian M T Spahn / Tatyana V Budkevich /
Abstract: Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes ...Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.
History
DepositionJul 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.0Dec 5, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 5, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 5, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 5, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 5, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 5, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 5, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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
Revision 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _em_admin.last_update / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 1.1Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A2: 28S ribosomal RNA
Bv: ap/P-site tRNA
Bx: mRNA
Bw: pe/E-site-tRNA
B1: 18S ribosomal RNA
BD: ribosomal protein uS3
BF: Ribosomal protein S5
BK: ribosomal protein eS10
BM: 40S ribosomal protein S12
BP: ribosomal protein uS19
BQ: ribosomal protein uS9
BR: ribosomal protein eS17
BS: ribosomal protein uS13
BT: ribosomal protein eS19
BU: ribosomal protein uS10
BZ: ribosomal protein eS25
Bc: Ribosomal protein S28
Bd: ribosomal protein uS14
Bf: Ribosomal protein S27a
Bg: ribosomal protein RACK 1
BA: ribosomal protein uS2
BB: 40S ribosomal protein S3a
BC: ribosomal protein uS5
BE: ribosomal protein eS4
BG: 40S ribosomal protein S6
BH: 40S ribosomal protein S7
BI: ribosomal protein eS8
BJ: Ribosomal protein S9 (Predicted)
BL: Ribosomal protein S11
BN: ribosomal protein uS15
BO: ribosomal protein uS11
BV: ribosomal protein eS21
BW: Ribosomal protein S15a
BX: Ribosomal protein S23
BY: ribosomal protein eS24
Ba: ribosomal protein eS26
Bb: ribosomal protein eS27
Be: ribosomal protein eS30
A3: 5.8S ribosomal RNA
A4: 5S ribosomal RNA
AA: Ribosomal protein L8
AB: ribosomal protein uL3
AC: ribosomal protein uL4
AD: ribosomal protein uL18
AE: ribosomal protein eL6
AF: ribosomal protein uL30
AG: ribosomal protein eL8
AH: ribosomal protein uL6
AI: Ribosomal protein L10 (Predicted)
AJ: Ribosomal protein L11
AL: ribosomal protein eL13
AM: ribosomal protein eL14
AN: Ribosomal protein L15
AO: ribosomal protein uL13
AP: ribosomal protein uL22
AQ: ribosomal protein eL18
AR: ribosomal protein eL19
AS: ribosomal protein eL20
AT: ribosomal protein eL21
AU: ribosomal protein eL22
AV: Ribosomal protein L23
AW: ribosomal protein eL24
AX: ribosomal protein uL23
AY: Ribosomal protein L26
AZ: 60S ribosomal protein L27
Aa: ribosomal protein uL15
Ab: ribosomal protein eL29
Ac: ribosomal protein eL30
Ad: ribosomal protein eL31
Ae: ribosomal protein eL32
Af: ribosomal protein eL33
Ag: ribosomal protein eL34
Ah: ribosomal protein uL29
Ai: ribosomal protein eL36
Aj: Ribosomal protein L37
Ak: ribosomal protein eL38
Al: ribosomal protein eL39
Am: ribosomal protein eL40
An: ribosomal protein eL41
Ao: ribosomal protein eL42
Ap: ribosomal protein eL43
At: ribosomal protein eL28
Au: Ribosomal protein
Aq: Ribosomal protein L12
AK: ribosomal protein uL10
Ct: eukaryotic elongation factor 2 (eEF2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,326,031419
Polymers3,317,23486
Non-polymers8,797333
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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RNA chain , 7 types, 7 molecules A2BvBxBwB1A3A4

#1: RNA chain 28S ribosomal RNA


Mass: 1170164.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: RNA chain ap/P-site tRNA


Mass: 24437.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#3: RNA chain mRNA


Mass: 3837.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage SP6 (virus) / Production host: Enterobacteria phage SP6 (virus)
#4: RNA chain pe/E-site-tRNA


Mass: 24533.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 176421
#5: RNA chain 18S ribosomal RNA


Mass: 551108.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: RNA chain 5.8S ribosomal RNA


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#40: RNA chain 5S ribosomal RNA


Mass: 38385.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Ribosomal protein ... , 72 types, 72 molecules BDBFBKBPBQBRBSBTBUBZBcBdBfBgBABCBEBIBJBLBNBOBVBWBXBYBaBbBeAA...

#6: Protein ribosomal protein uS3


Mass: 24357.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: Protein Ribosomal protein S5


Mass: 21424.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#8: Protein ribosomal protein eS10


Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#10: Protein ribosomal protein uS19


Mass: 14273.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#11: Protein ribosomal protein uS9


Mass: 15765.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein ribosomal protein eS17


Mass: 14447.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#13: Protein ribosomal protein uS13


Mass: 16383.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#14: Protein ribosomal protein eS19


Mass: 15822.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein ribosomal protein uS10


Mass: 11029.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#16: Protein ribosomal protein eS25


Mass: 9801.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#17: Protein Ribosomal protein S28


Mass: 7007.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#18: Protein ribosomal protein uS14


Mass: 6121.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#19: Protein Ribosomal protein S27a


Mass: 8645.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#20: Protein ribosomal protein RACK 1


Mass: 34726.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#21: Protein ribosomal protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 24245.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#23: Protein ribosomal protein uS5


Mass: 24574.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein ribosomal protein eS4


Mass: 28893.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein ribosomal protein eS8


Mass: 24132.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein Ribosomal protein S9 (Predicted)


Mass: 21222.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#29: Protein Ribosomal protein S11


Mass: 17910.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#30: Protein ribosomal protein uS15


Mass: 17057.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#31: Protein ribosomal protein uS11


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#32: Protein ribosomal protein eS21


Mass: 8863.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#33: Protein Ribosomal protein S15a


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#34: Protein Ribosomal protein S23


Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#35: Protein ribosomal protein eS24


Mass: 14489.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: Protein ribosomal protein eS26


Mass: 11087.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: Protein ribosomal protein eS27


Mass: 9000.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: Protein ribosomal protein eS30


Mass: 6239.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein Ribosomal protein L8


Mass: 27456.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#42: Protein ribosomal protein uL3


Mass: 45222.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein ribosomal protein uL4


Mass: 41171.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein ribosomal protein uL18


Mass: 34091.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#45: Protein ribosomal protein eL6


Mass: 22262.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: Protein ribosomal protein uL30


Mass: 27733.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: Protein ribosomal protein eL8


Mass: 26724.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#48: Protein ribosomal protein uL6


Mass: 21770.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein Ribosomal protein L10 (Predicted)


Mass: 24381.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#50: Protein Ribosomal protein L11


Mass: 19270.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#51: Protein ribosomal protein eL13


Mass: 23574.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein ribosomal protein eL14


Mass: 16220.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein Ribosomal protein L15


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#54: Protein ribosomal protein uL13


Mass: 22820.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#55: Protein ribosomal protein uL22


Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#56: Protein ribosomal protein eL18


Mass: 21556.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: Protein ribosomal protein eL19


Mass: 21742.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#58: Protein ribosomal protein eL20


Mass: 20661.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#59: Protein ribosomal protein eL21


Mass: 18276.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#60: Protein ribosomal protein eL22


Mass: 11481.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#61: Protein Ribosomal protein L23


Mass: 13828.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#62: Protein ribosomal protein eL24


Mass: 14087.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#63: Protein ribosomal protein uL23


Mass: 13614.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#64: Protein Ribosomal protein L26


Mass: 15161.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#66: Protein ribosomal protein uL15


Mass: 16473.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#67: Protein ribosomal protein eL29


Mass: 7996.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#68: Protein ribosomal protein eL30


Mass: 11500.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#69: Protein ribosomal protein eL31


Mass: 12506.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#70: Protein ribosomal protein eL32


Mass: 15179.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUN8
#71: Protein ribosomal protein eL33


Mass: 12433.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein ribosomal protein eL34


Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: Protein ribosomal protein uL29


Mass: 14462.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#74: Protein ribosomal protein eL36


Mass: 11373.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein Ribosomal protein L37


Mass: 9864.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#76: Protein ribosomal protein eL38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#77: Protein/peptide ribosomal protein eL39


Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYU7
#78: Protein/peptide ribosomal protein eL40


Mass: 5957.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#79: Protein/peptide ribosomal protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#80: Protein ribosomal protein eL42


Mass: 12345.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T040
#81: Protein ribosomal protein eL43


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#82: Protein ribosomal protein eL28


Mass: 13991.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: Protein Ribosomal protein L12


Mass: 16290.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#85: Protein ribosomal protein uL10


Mass: 22217.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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40S ribosomal protein ... , 4 types, 4 molecules BMBBBGBH

#9: Protein 40S ribosomal protein S12


Mass: 13393.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#22: Protein 40S ribosomal protein S3a


Mass: 24660.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#25: Protein 40S ribosomal protein S6


Mass: 26913.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#26: Protein 40S ribosomal protein S7


Mass: 20990.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0

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Protein , 3 types, 3 molecules AZAuCt

#65: Protein 60S ribosomal protein L27


Mass: 15647.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#83: Protein Ribosomal protein


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8
#86: Protein eukaryotic elongation factor 2 (eEF2)


Mass: 95056.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 3 types, 333 molecules

#87: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 327 / Source method: obtained synthetically / Formula: Mg
#88: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#89: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1translocation intermediate TI-POST-1RIBOSOME#1-#860MULTIPLE SOURCES
2RibosomeCOMPLEX#1-#2, #5-#861NATURAL
3mRNACOMPLEX#31RECOMBINANT
4tRNACOMPLEX#41NATURAL
Molecular weightValue: 4.3 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
42Oryctolagus cuniculus (rabbit)9986
23Enterobacteria phage SP6 (virus)194966
54Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)Organism: Enterobacteria phage SP6 (virus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 5 sec. / Electron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 270000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32386 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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