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

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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 / homologyRibosomal protein L1-like / Ribosomal protein S8 superfamily / Ribosomal protein L15e core domain superfamily / 30s ribosomal protein S13, C-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily ...Ribosomal protein L1-like / Ribosomal protein S8 superfamily / Ribosomal protein L15e core domain superfamily / 30s ribosomal protein S13, C-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / 40S ribosomal protein S11, N-terminal / WD40-repeat-containing domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L32e superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S7 domain / Ribosomal protein L2, archaeal-type / Ribosomal protein L24e/L24 superfamily / Ribosomal protein S7, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L11, C-terminal / Ribosomal protein L39e domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein S15P / Ribosomal protein L24e, conserved site / Ribosomal protein L31e domain superfamily / S27a-like superfamily / Ribosomal protein L27e superfamily / Ribosomal protein S13, conserved site / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S7e / S4 domain / Ribosomal protein S27a / Ribosomal protein L32 / Ribosomal L27e protein family / Ribosomal L37ae protein family / Ribosomal protein L37e / S25 ribosomal protein / Plectin/S10 domain / Ribosomal protein L11, N-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal_S17 N-terminal / Ribosomal protein L24e / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L14 signature. / Ribosomal protein L39e signature. / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ubiquitin domain signature. / Ribosomal protein L5 signature. / Ribosomal protein L11 signature. / Ribosomal protein S15 signature. / Ribosomal protein L2 signature. / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S28e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S17 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L14p/L23e / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein S14p/S29e / Ribosomal protein L5 / Ribosomal protein L11, RNA binding domain / Ribosomal protein S15 / WD domain, G-beta repeat
Function and homology information
Specimen sourceEnterobacteria phage SP6 (bacteriophage)
Oryctolagus cuniculus (rabbit)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
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.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2018 / Release: Dec 5, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 5, 2018Structure modelrepositoryInitial release
1.1Dec 19, 2018Structure modelData collection / Database referencescitation / citation_author_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

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Structure visualization

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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
Polyers3,317,23486
Non-polymers8,797333
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: none
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: (natural) Oryctolagus cuniculus (rabbit)
#2: RNA chain ap/P-site tRNA


Mass: 24437.535 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#3: RNA chain mRNA / Messenger RNA


Mass: 3837.328 Da / Num. of mol.: 1
Source: (gene. exp.) Enterobacteria phage SP6 (bacteriophage)
Production host: Enterobacteria phage SP6 (bacteriophage)
#4: RNA chain pe/E-site-tRNA


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


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


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


Mass: 38385.750 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)

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

#6: Protein/peptide ribosomal protein uS3 /


Mass: 24357.590 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: Protein/peptide Ribosomal protein S5 /


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


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


Mass: 14273.879 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#11: Protein/peptide ribosomal protein uS9 /


Mass: 15765.480 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein/peptide ribosomal protein eS17 /


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


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


Mass: 15822.219 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein/peptide ribosomal protein uS10 /


Mass: 11029.072 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#16: Protein/peptide ribosomal protein eS25 /


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


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


Mass: 6121.210 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#19: Protein/peptide Ribosomal protein S27a / Ribosome


Mass: 8645.277 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#20: Protein/peptide ribosomal protein RACK 1 / Ribosome


Mass: 34726.164 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#21: Protein/peptide ribosomal protein uS2 / / 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: (natural) Oryctolagus cuniculus (rabbit)
#23: Protein/peptide ribosomal protein uS5 /


Mass: 24574.971 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein/peptide ribosomal protein eS4 /


Mass: 28893.043 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein/peptide ribosomal protein eS8 /


Mass: 24132.191 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein/peptide Ribosomal protein S9 (Predicted) / Ribosome


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


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


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


Mass: 14544.659 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#32: Protein/peptide ribosomal protein eS21 /


Mass: 8863.111 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#33: Protein/peptide Ribosomal protein S15a / Ribosome


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


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


Mass: 14489.176 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: Protein/peptide ribosomal protein eS26 /


Mass: 11087.117 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: Protein/peptide ribosomal protein eS27 /


Mass: 9000.570 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: Protein/peptide ribosomal protein eS30 /


Mass: 6239.447 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein/peptide Ribosomal protein L8 /


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


Mass: 45222.949 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein/peptide ribosomal protein uL4 /


Mass: 41171.547 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein/peptide ribosomal protein uL18 /


Mass: 34091.371 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#45: Protein/peptide ribosomal protein eL6 /


Mass: 22262.428 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: Protein/peptide ribosomal protein uL30 /


Mass: 27733.146 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: Protein/peptide ribosomal protein eL8 /


Mass: 26724.568 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#48: Protein/peptide ribosomal protein uL6 /


Mass: 21770.355 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein/peptide Ribosomal protein L10 (Predicted) / Ribosome


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


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


Mass: 23574.697 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein/peptide ribosomal protein eL14 /


Mass: 16220.309 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein/peptide Ribosomal protein L15 /


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


Mass: 22820.395 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#55: Protein/peptide ribosomal protein uL22 /


Mass: 17757.627 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#56: Protein/peptide ribosomal protein eL18 /


Mass: 21556.482 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: Protein/peptide ribosomal protein eL19 /


Mass: 21742.146 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#58: Protein/peptide ribosomal protein eL20 /


Mass: 20661.340 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#59: Protein/peptide ribosomal protein eL21 /


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


Mass: 11481.248 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#61: Protein/peptide Ribosomal protein L23 /


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


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


Mass: 13614.023 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#64: Protein/peptide Ribosomal protein L26 /


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


Mass: 16473.340 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#67: Protein/peptide ribosomal protein eL29 /


Mass: 7996.388 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#68: Protein/peptide ribosomal protein eL30 /


Mass: 11500.556 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#69: Protein/peptide ribosomal protein eL31 /


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


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


Mass: 12433.548 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein/peptide ribosomal protein eL34 /


Mass: 12994.621 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: Protein/peptide ribosomal protein uL29 /


Mass: 14462.429 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#74: Protein/peptide ribosomal protein eL36 /


Mass: 11373.708 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein/peptide Ribosomal protein L37 /


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


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


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


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


Mass: 3473.451 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#80: Protein/peptide ribosomal protein eL42 /


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


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


Mass: 13991.366 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: Protein/peptide Ribosomal protein L12 /


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


Mass: 22217.840 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)

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

#9: Protein/peptide 40S ribosomal protein S12 /


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


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


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


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

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Protein/peptide , 3 types, 3 molecules AZAuCt

#65: Protein/peptide 60S ribosomal protein L27 /


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


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


Mass: 95056.734 Da / Num. of mol.: 1 / 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 / Formula: Mg / Magnesium
#88: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 522.196 Da / Num. of mol.: 1 / Formula: C10H17N6O13P3
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 / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1translocation intermediate TI-POST-1RIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 860MULTIPLE SOURCES
2RibosomeCOMPLEX1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 861NATURAL
3mRNACOMPLEX31RECOMBINANT
4tRNACOMPLEX41NATURAL
Molecular weightValue: 4.3 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
429986Oryctolagus cuniculus (rabbit)
23194966Enterobacteria phage SP6 (bacteriophage)
544932Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)Organism: Enterobacteria phage SP6 (bacteriophage)
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
MicroscopyMicroscope model: 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 selectionNumber of particles selected: 270000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 32386 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

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