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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)
  • mRNAMessenger RNA
  • pe/E-site-tRNA
KeywordsRIBOSOME / translocation rabbit ribosome / 80S / eEF2 / head swivel / rotation
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation
Similarity search - Function
Ribosomal protein S12e signature. / Ribosomal protein S27a / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Ribosomal protein L44 / Plectin/S10 domain / Ribosomal L27e protein family / Ribosomal protein L1 signature. / Ribosomal protein S17e signature. / Ribosomal protein S28e ...Ribosomal protein S12e signature. / Ribosomal protein S27a / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Ribosomal protein L44 / Plectin/S10 domain / Ribosomal L27e protein family / Ribosomal protein L1 signature. / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal protein L44e signature. / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal L37ae protein family / Ribosomal protein S3Ae signature. / Ribosomal protein L24e signature. / Ribosomal protein L32e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L31e / Ribosomal protein S6e signature. / Ribosomal L39 protein / Ribosomal protein S28e signature. / Ribosomal protein L37e / Ribosomal L15 / Ribosomal protein L31e signature. / Ribosomal protein L1p/L10e family / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L32e / Ribosomal protein L32e superfamily / Ribosomal_L32e / Ribosomal protein L32e signature. / Ribosomal protein L32 / Ribosomal protein L15e signature. / Ribosomal protein L21e signature. / Ribosomal protein L37e signature. / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S14 signature. / Ribosomal protein L5 signature. / Ribosomal protein L5 / Ribosomal protein S4/S9 N-terminal domain / ribosomal L5P family C-terminus / Ribosomal protein L16p/L10e / Ribosomal protein S13/S18 / Ribosomal protein S14p/S29e / Ribosomal protein S7 signature. / Ribosomal protein S8 / Ribosomal protein S17 signature. / Ribosomal protein S13 signature. / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / S4 domain / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / Ribosomal protein S7p/S5e / S4 RNA-binding domain profile. / Ribosomal protein S12/S23 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal protein L14 signature. / Ubiquitin domain profile. / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S12 signature. / Ribosomal protein L24 signature. / Ribosomal protein L14p/L23e / KOW motif / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Winged helix-like DNA-binding domain superfamily
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 / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Ribosomal protein L32 / 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 1.1Dec 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

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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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
Water0
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 / Messenger RNA


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 / Ribosome


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 / Ribosome


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) / Ribosome


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 / Ribosome


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) / Ribosome


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 / 5'-Guanylyl imidodiphosphate


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

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Experimental details

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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
3mRNAMessenger RNACOMPLEX#31RECOMBINANT
4tRNATransfer RNACOMPLEX#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 FIELDBright-field microscopy
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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