6GZ5

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.

Flis, J.Holm, M.Rundlet, E.J.Loerke, J.Hilal, T.Dabrowski, M.Burger, J.Mielke, T.Blanchard, S.C.Spahn, C.M.T.Budkevich, T.V.

(2018) Cell Rep 25: 2676-2688.e7

  • DOI: 10.1016/j.celrep.2018.11.040
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Translocation moves the tRNA 2 ⋅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 subst ...

    Translocation moves the tRNA 2 ⋅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 2 ⋅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.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: tetyana.budkevych@charite.de.



Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS3BD220Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS7BF190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS10BK98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS12BM120Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS19BP120Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS9BQ139Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS17BR125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS13BS139Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS19BT143Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS10BU97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS25BZ86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS28Bc62Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS14Bd51Salmonella virus SP6Mutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS31Bf73Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RACK 1Bg314Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS2BA215Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS1BB212Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS5BC222Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS4BE257Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS6BG232Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS7BH183Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS8BI207Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS4BJ179Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS17BL153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS15BN149Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS11BO136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS21BV81Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS8BW129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS24BY125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS26Ba97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS27Bb80Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS30Be55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL2AA252Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL3AB394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL4AC363Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL18AD294Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL6AE194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL30AF234Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL8AG234Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL6AH191Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL16AI208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL5AJ169Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL13AL205Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL14AM139Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL15AN203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL13AO195Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL22AP153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL18AQ187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL19AR181Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL20AS175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL21AT157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL22AU99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL14AV129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL24AW121Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL23AX117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL24AY127Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL27AZ134Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL15Aa147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL29Ab68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL30Ac103Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL31Ad106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL32Ae129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL33Af109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL34Ag114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL29Ah122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL36Ai97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL38Ak69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL39Al50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL40Am50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL41An25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL42Ao105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL43Ap91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL28At122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL1Au217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL11Aq151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL10AK202Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
eukaryotic elongation factor 2 (eEF2)Ct853Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS12BX141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL37Aj84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
28S ribosomal RNAA23612Oryctolagus cuniculus

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Entity ID: 2
MoleculeChainsLengthOrganism
P/P-site-tRNABv76Oryctolagus cuniculus
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Entity ID: 3
MoleculeChainsLengthOrganism
mRNABx11Salmonella virus SP6

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Entity ID: 4
MoleculeChainsLengthOrganism
E/E-site-tRNABw76Saccharomyces cerevisiae

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Entity ID: 5
MoleculeChainsLengthOrganism
18S ribosomal RNAB11708Oryctolagus cuniculus

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Entity ID: 39
MoleculeChainsLengthOrganism
5.8S ribosomal RNAA3157Oryctolagus cuniculus

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Entity ID: 40
MoleculeChainsLengthOrganism
5S ribosomal RNAA4119Oryctolagus cuniculus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

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Ct
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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Aj, Ao, Ap, Ba, Bd
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A2, A3, A4, AA, AC, AL, AO, AP, AY, An, B1, BD, Ba, Bx
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DDE
Query on DDE
CtL-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyDFG SFB 740
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM079238
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM115327-Tan

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references