6WDI

Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure IV-B2)


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 1.3 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 584: 640-645

  • DOI: https://doi.org/10.1038/s41586-020-2447-x
  • Primary Citation of Related Structures:  
    6WD0, 6WD1, 6WD2, 6WD3, 6WD4, 6WD5, 6WD6, 6WD7, 6WD8, 6WD9, 6WDA, 6WDB, 6WDC, 6WDD, 6WDE, 6WDF, 6WDG, 6WDH, 6WDI, 6WDJ, 6WDK, 6WDL, 6WDM

  • 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, 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2A [auth b]271Escherichia coliMutation(s): 0 
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Entity ID: 2
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50S ribosomal protein L3B [auth c]209Escherichia coliMutation(s): 0 
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Entity ID: 3
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50S ribosomal protein L4C [auth d]201Escherichia coliMutation(s): 0 
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Entity ID: 4
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50S ribosomal protein L5D [auth e]177Escherichia coliMutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L6E [auth f]176Escherichia coliMutation(s): 0 
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50S ribosomal protein L9F [auth g]149Escherichia coliMutation(s): 0 
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50S ribosomal protein L10G [auth h]131Escherichia coliMutation(s): 0 
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50S ribosomal protein L11H [auth i]141Escherichia coliMutation(s): 0 
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50S ribosomal protein L13I [auth j]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L15K [auth l]143Escherichia coliMutation(s): 0 
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50S ribosomal protein L16L [auth m]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17M [auth n]120Escherichia coliMutation(s): 0 
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50S ribosomal protein L18N [auth o]116Escherichia coliMutation(s): 0 
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50S ribosomal protein L21Q [auth r]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22R [auth s]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23S [auth t]93Escherichia coliMutation(s): 0 
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50S ribosomal protein L24T [auth u]102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25U [auth v]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27V [auth w]75Escherichia coliMutation(s): 0 
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50S ribosomal protein L28W [auth x]77Escherichia coliMutation(s): 0 
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50S ribosomal protein L30Y [auth z]58Escherichia coliMutation(s): 0 
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50S ribosomal protein L34BA [auth D]46Escherichia coliMutation(s): 0 
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30S ribosomal protein S3FA [auth H]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S4GA [auth I]205Escherichia coliMutation(s): 0 
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30S ribosomal protein S5HA [auth J]157Escherichia coliMutation(s): 0 
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30S ribosomal protein S6IA [auth K]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S8KA [auth M]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S10MA [auth O]98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11NA [auth P]116Escherichia coliMutation(s): 0 
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30S ribosomal protein S12OA [auth Q]123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13PA [auth R]114Escherichia coliMutation(s): 0 
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30S ribosomal protein S14QA [auth S]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15RA [auth T]88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16SA [auth U]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17TA [auth V]80Escherichia coliMutation(s): 0 
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UniProt GroupP0AG63
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18UA [auth W]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19VA [auth X]79Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20WA [auth Y]85Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21XA [auth Z]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1YA [auth a]223Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7L0 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains LengthOrganismImage
16S ribosomal RNAZA [auth 3]1,539Escherichia coli
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Entity ID: 53
MoleculeChains LengthOrganismImage
23S ribosomal RNAAB [auth 1]2,903Escherichia coli
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Entity ID: 54
MoleculeChains LengthOrganismImage
5S ribosomal RNABB [auth 2]120Escherichia coli
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Entity ID: 55
MoleculeChains LengthOrganismImage
tRNAfMetCB [auth 5],
DB [auth 6]
77Escherichia coli
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Entity ID: 56
MoleculeChains LengthOrganismImage
mRNAEB [auth 4]18Escherichia coli
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Entity ID: 57
MoleculeChains LengthOrganismImage
tRNAPheFB [auth 7]76Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download Ideal Coordinates CCD File 
GB [auth 5]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCNS
MODEL REFINEMENTRSRef
MODEL REFINEMENTPHENIX
RECONSTRUCTIONFREALIGN

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2020-09-09
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references