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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

21619

6wd0

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

21620

6wd1

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

21621

6wd2

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

21622

6wd3

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

21623

6wd4

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

21624

6wd5

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

21625

6wd6

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

21626

6wd7

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

21627

6wd8

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

21628

6wd9

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

21629

6wda

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

21630

6wdb

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

21631

6wdc

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

21632

6wdd

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

21633

6wde

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

21634

6wdf

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

21635

6wdg

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

21636

6wdh

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

21637

6wdi

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

21638

6wdj

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

21639

6wdk

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

21640

6wdl

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

21641

6wdm

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 / N-Formylmethionine

ChemComp-PHE:
PHENYLALANINE / Phenylalanine

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

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

ChemComp-MET:
METHIONINE / 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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