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TitleCryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading.
Journal, issue, pagesNature, Vol. 584, Issue 7822, Page 640-645, Year 2020
Publish dateJul 1, 2020
AuthorsAnna B Loveland / Gabriel Demo / Andrei A Korostelev /
PubMed AbstractRibosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu. To understand the molecular mechanism of this proofreading step it is necessary ...Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu. To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation, which has remained a challenge. 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 and in proofreading states, which together govern the efficient rejection of incorrect tRNA.
External linksNature / PubMed:32612237 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 4.3 Å
Structure data

EMDB-21619, PDB-6wd0:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure I-A)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-21620, PDB-6wd1:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure I-B)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-21621, PDB-6wd2:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-A)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-21622, PDB-6wd3:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-B1)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-21623, PDB-6wd4:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-B2)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-21624, PDB-6wd5:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-C1)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-21625, PDB-6wd6:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-C2)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-21626: Cryo-EM of elongating ribosome with EF-Tu-GTP elucidates tRNA proofreading (Cognate Structure II-D)
PDB-6wd7: Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-D)
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-21627, PDB-6wd8:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure III-A)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-21628, PDB-6wd9:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure III-B)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-21629, PDB-6wda:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure III-C)
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-21630, PDB-6wdb:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure IV-A)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-21631, PDB-6wdc:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure IV-B)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-21632, PDB-6wdd:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure V-A)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-21633, PDB-6wde:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure V-B)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-21634, PDB-6wdf:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure VI-A)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-21635, PDB-6wdg:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure VI-B)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-21636, PDB-6wdh:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure IV-B1)
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-21637, PDB-6wdi:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure IV-B2)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-21638, PDB-6wdj:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure V-A1)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-21639, PDB-6wdk:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure V-A2)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-21640, PDB-6wdl:
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure V-B1)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-21641: Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading(Non-cognate Structure V-B2)
PDB-6wdm: Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure V-B2)
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-FME:
N-FORMYLMETHIONINE

ChemComp-PHE:
PHENYLALANINE

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-MET:
METHIONINE

Source
  • escherichia coli (E. coli)
  • Escherichia coli
  • escherichia coli (strain k12) (bacteria)
  • Eschericia coli (E. coli)
  • escherichia coli k-12 (bacteria)
KeywordsRIBOSOME / EF-Tu / tRNA / Ribosome/RNA / Ribosome-RNA complex

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