7PJW

Structure of the 70S-EF-G-GDP-Pi ribosome complex with tRNAs in hybrid state 2 (H2-EF-G-GDP-Pi)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural mechanism of GTPase-powered ribosome-tRNA movement.

Petrychenko, V.Peng, B.Z.de A P Schwarzer, A.C.Peske, F.Rodnina, M.V.Fischer, N.

(2021) Nat Commun 12: 5933-5933

  • DOI: https://doi.org/10.1038/s41467-021-26133-x
  • Primary Citation of Related Structures:  
    7PJT, 7PJU, 7PJV, 7PJW, 7PJX, 7PJY, 7PJZ

  • PubMed Abstract: 

    GTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome along the mRNA. The key unresolved question is how GTP hydrolysis drives molecular movement. Here, we visualize the GTPase-powered step of ongoing translocation by time-resolved cryo-EM. EF-G in the active GDP-Pi form stabilizes the rotated conformation of ribosomal subunits and induces twisting of the sarcin-ricin loop of the 23 S rRNA. Refolding of the GTPase switch regions upon Pi release initiates a large-scale rigid-body rotation of EF-G pivoting around the sarcin-ricin loop that facilitates back rotation of the ribosomal subunits and forward swiveling of the head domain of the small subunit, ultimately driving tRNA forward movement. The findings demonstrate how a GTPase orchestrates spontaneous thermal fluctuations of a large RNA-protein complex into force-generating molecular movement.


  • Organizational Affiliation

    Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Escherichia coliMutation(s): 0 
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Entity ID: 2
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50S ribosomal protein L33B [auth 1]55Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34C [auth 2]46Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35D [auth 3]65Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36E [auth 4]38Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10F [auth 5]165Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31G [auth 6]70Escherichia coliMutation(s): 0 
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50S ribosomal protein L2J [auth C]273Escherichia coliMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L3K [auth D]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4L [auth E]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5M [auth F]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6N [auth G]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L9O [auth H]149Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11P [auth I]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L13Q [auth J]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14R [auth K]123Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15S [auth L]144Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16T [auth M]136Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17U [auth N]127Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18V [auth O]117Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L19W [auth P]115Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20X [auth Q]118Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Y [auth R]103Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Z [auth S]110Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23AA [auth T]100Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24BA [auth U]104Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25CA [auth V]94Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27DA [auth W]85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28EA [auth X]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29FA [auth Y]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30GA [auth Z]59Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth b]240Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth c]233Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth d]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5LA [auth e]167Escherichia coliMutation(s): 0 
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30S ribosomal protein S6MA [auth f]135Escherichia coliMutation(s): 0 
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30S ribosomal protein S7NA [auth g]179Escherichia coliMutation(s): 0 
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30S ribosomal protein S8OA [auth h]130Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth i]130Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth j]103Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth k]129Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth l]124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13TA [auth m]118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14UA [auth n]102Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15VA [auth o]89Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16WA [auth p]82Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth q]84Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth r]75Escherichia coliMutation(s): 0 
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Find proteins for C3SFP7 (Escherichia coli)
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Go to UniProtKB:  C3SFP7
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UniProt GroupC3SFP7
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth s]92Escherichia coliMutation(s): 0 
UniProt
Find proteins for C3SQW2 (Escherichia coli)
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UniProt GroupC3SQW2
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth t]87Escherichia coliMutation(s): 0 
UniProt
Find proteins for C3TRH7 (Escherichia coli)
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UniProt GroupC3TRH7
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21BB [auth u]71Escherichia coliMutation(s): 0 
UniProt
Find proteins for C3STZ7 (Escherichia coli)
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UniProt GroupC3STZ7
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor GEB [auth x]704Escherichia coliMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptide (FME-PHE)FB [auth y]2Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains LengthOrganismImage
23S ribosomal RNAH [auth A]2,903Escherichia coli
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Entity ID: 9
MoleculeChains LengthOrganismImage
5S ribosomal RNAI [auth B]120Escherichia coli
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Entity ID: 34
MoleculeChains LengthOrganismImage
16S ribosomal RNAHA [auth a]1,542Escherichia coli
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Entity ID: 55
MoleculeChains LengthOrganismImage
P-site tRNA(fMet)CB [auth v]77Escherichia coli
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Entity ID: 56
MoleculeChains LengthOrganismImage
P-site fMet-Phe-tRNA(Phe)DB [auth w]76Escherichia coli
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Entity ID: 59
MoleculeChains LengthOrganismImage
mRNAGB [auth z]33Escherichia coli
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
FB [auth y]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX16
MODEL REFINEMENTISOLDE1.1.0
MODEL REFINEMENTCoot0.9.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyLeibniz Prize (to M.V.R.) & SFB 860
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release