6WDE

Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure V-B)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading.

Loveland, A.B.Demo, G.Korostelev, A.A.

(2020) Nature 

  • DOI: 10.1038/s41586-020-2447-x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu 1 . To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation ...

    Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu 1 . To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation, which has remained a challenge 2-4 . Here we use time-resolved cryogenic electron microscopy to reveal 33 ribosomal states after the delivery of aminoacyl-tRNA by EF-Tu•GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding centre dynamically monitors codon-anticodon interactions before and after GTP hydrolysis. GTP hydrolysis enables the GTPase domain of EF-Tu to extend away, releasing EF-Tu from tRNA. The 30S subunit then locks cognate tRNA in the decoding centre and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase centre. By contrast, the decoding centre fails to lock near-cognate tRNA, enabling the dissociation of near-cognate tRNA both during initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between ribosomes in initial selection states 5,6 and in proofreading states, which together govern the efficient rejection of incorrect tRNA.


    Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. andrei.korostelev@umassmed.edu.



Macromolecules

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Entity ID: 1
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50S ribosomal protein L2b271Escherichia coliMutation(s): 0 
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50S ribosomal protein L3c209Escherichia coliMutation(s): 0 
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50S ribosomal protein L9g149Escherichia coliMutation(s): 0 
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50S ribosomal protein L10h131Escherichia coliMutation(s): 0 
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50S ribosomal protein L11i141Escherichia coliMutation(s): 0 
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50S ribosomal protein L18o116Escherichia coliMutation(s): 0 
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50S ribosomal protein L32B56Escherichia coliMutation(s): 0 
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50S ribosomal protein L33C50Escherichia coliMutation(s): 0 
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50S ribosomal protein L34D46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35E64Escherichia coliMutation(s): 0 
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50S ribosomal protein L36F38Escherichia coliMutation(s): 0 
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30S ribosomal protein S2G225Escherichia coliMutation(s): 0 
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30S ribosomal protein S3H206Escherichia coliMutation(s): 0 
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30S ribosomal protein S4I205Escherichia coliMutation(s): 0 
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30S ribosomal protein S5J157Escherichia coliMutation(s): 0 
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30S ribosomal protein S8M129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9N127Escherichia coliMutation(s): 0 
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30S ribosomal protein S10O98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11P116Escherichia coliMutation(s): 0 
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30S ribosomal protein S12Q123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13R114Escherichia coliMutation(s): 0 
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30S ribosomal protein S14S100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15T88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16U82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17V80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18W65Escherichia coliMutation(s): 0 
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30S ribosomal protein S19X79Escherichia coliMutation(s): 0 
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30S ribosomal protein S20Y85Escherichia coliMutation(s): 0 
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30S ribosomal protein S21Z65Escherichia coliMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1a223Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChainsLengthOrganism
16S ribosomal RNA31539Escherichia coli

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Entity ID: 53
MoleculeChainsLengthOrganism
23S ribosomal RNA12903Escherichia coli

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Entity ID: 54
MoleculeChainsLengthOrganism
5S ribosomal RNA2120Escherichia coli

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Entity ID: 55
MoleculeChainsLengthOrganism
tRNAfMet5, 677Escherichia coli
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Entity ID: 56
MoleculeChainsLengthOrganism
mRNA418Escherichia coli K-12

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Entity ID: 57
MoleculeChainsLengthOrganism
tRNAPhe777Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

Download CCD File 
7
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
MET
Query on MET

Download CCD File 
7
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM106105
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM107465
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127094

Revision History 

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references