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TitleStructural characterization of mRNA-tRNA translocation intermediates.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 109, Issue 16, Page 6094-6099, Year 2012
Publish dateApr 17, 2012
AuthorsXabier Agirrezabala / Hstau Y Liao / Eduard Schreiner / Jie Fu / Rodrigo F Ortiz-Meoz / Klaus Schulten / Rachel Green / Joachim Frank /
PubMed AbstractCryo-EM analysis of a wild-type Escherichia coli pretranslocational sample has revealed the presence of previously unseen intermediate substates of the bacterial ribosome during the first phase of ...Cryo-EM analysis of a wild-type Escherichia coli pretranslocational sample has revealed the presence of previously unseen intermediate substates of the bacterial ribosome during the first phase of translocation, characterized by intermediate intersubunit rotations, L1 stalk positions, and tRNA configurations. Furthermore, we describe the domain rearrangements in quantitative terms, which has allowed us to characterize the processivity and coordination of the conformational reorganization of the ribosome, along with the associated changes in tRNA ribosome-binding configuration. The results are consistent with the view of the ribosome as a molecular machine employing Brownian motion to reach a functionally productive state via a series of substates with incremental changes in conformation.
External linksProc Natl Acad Sci U S A / PubMed:22467828 / PubMed Central
MethodsEM (single particle)
Resolution11.5 - 14.7 Å
Structure data

5359

4v6o

EMDB-5359: New mRNA-tRNA translocation intermediates revealed by cryoEM: Class 4A (partially rotated (I) 70S ribosome with A-site and P-site tRNAs)
PDB-4v6o: Structural characterization of mRNA-tRNA translocation intermediates (class 4a of the six classes)
Method: EM (single particle) / Resolution: 14.7 Å

5360

4v6s

EMDB-5360: New mRNA-tRNA translocation intermediates revealed by cryoEM: Class 3 (unrotated 70S ribosome with P-site tRNA)
PDB-4v6s: Structural characterization of mRNA-tRNA translocation intermediates (class 3 of the six classes)
Method: EM (single particle) / Resolution: 13.1 Å

5361

4v6n

EMDB-5361: New mRNA-tRNA translocation intermediates revealed by cryoEM: Class 2 (unrotated 70S ribosome with A-site and P-site tRNAs)
PDB-4v6n: Structural characterization of mRNA-tRNA translocation intermediates (50S ribosome of class2 of the six classes)
Method: EM (single particle) / Resolution: 12.1 Å

5362

4v6r

EMDB-5362: New mRNA-tRNA translocation intermediates revealed by cryoEM: Class 6 (rotated 70S ribosome with A-site and P-site tRNAs)
PDB-4v6r: Structural characterization of mRNA-tRNA translocation intermediates (class 6 of the six classes)
Method: EM (single particle) / Resolution: 11.5 Å

5363

4v6q

EMDB-5363: New mRNA-tRNA translocation intermediates revealed by cryoEM: Class 5 (rotated 70S ribosome with A-site and P-site tRNAs)
PDB-4v6q: Structural characterization of mRNA-tRNA translocation intermediates (class 5 of the six classes)
Method: EM (single particle) / Resolution: 11.5 Å

5364

4v6p

EMDB-5364: New mRNA-tRNA translocation intermediates revealed by cryoEM: Class 4B (partially rotated (II) 70S ribosome with A-site and P-site tRNAs)
PDB-4v6p: Structural characterization of mRNA-tRNA translocation intermediates (class 4b of the six classes)
Method: EM (single particle) / Resolution: 13.5 Å

Chemicals

ChemComp-FME:
N-FORMYLMETHIONINE / N-Formylmethionine

ChemComp-TRP:
TRYPTOPHAN / Tryptophan

Source
  • escherichia coli (E. coli)
  • sulfolobus acidocaldarius (acidophilic)
KeywordsRIBOSOME / cryoelectron microscopy / molecular dynamics flexible fitting / ratchet-like rotation

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