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TitleRegulation of the protein-conducting channel by a bound ribosome.
Journal, issue, pagesStructure, Vol. 17, Issue 11, Page 1453-1464, Year 2009
Publish dateNov 11, 2009
AuthorsJames Gumbart / Leonardo G Trabuco / Eduard Schreiner / Elizabeth Villa / Klaus Schulten /
PubMed AbstractDuring protein synthesis, it is often necessary for the ribosome to form a complex with a membrane-bound channel, the SecY/Sec61 complex, in order to translocate nascent proteins across a cellular ...During protein synthesis, it is often necessary for the ribosome to form a complex with a membrane-bound channel, the SecY/Sec61 complex, in order to translocate nascent proteins across a cellular membrane. Structural data on the ribosome-channel complex are currently limited to low-resolution cryo-electron microscopy maps, including one showing a bacterial ribosome bound to a monomeric SecY complex. Using that map along with available atomic-level models of the ribosome and SecY, we have determined, through molecular dynamics flexible fitting (MDFF), an atomic-resolution model of the ribosome-channel complex. We characterized computationally the sites of ribosome-SecY interaction within the complex and determined the effect of ribosome binding on the SecY channel. We also constructed a model of a ribosome in complex with a SecY dimer by adding a second copy of SecY to the MDFF-derived model. The study involved 2.7-million-atom simulations over altogether nearly 50 ns.
External linksStructure / PubMed:19913480 / PubMed Central
MethodsEM (single particle)
Resolution9.6 Å
Structure data

PDB-4v7i:
Ribosome-SecY complex.
Method: ELECTRON MICROSCOPY / Resolution: 9.6 Å

Source
  • escherichia coli (E. coli)
  • methanocaldococcus jannaschii (archaea)
  • escherichia coli k-12 (bacteria)
KeywordsRIBOSOME / RIBOSOME-SECY COMPLEX / PROTEIN TRANSLOCATION / Cell membrane / Membrane / Protein transport / Translocation / Transmembrane / Transport / Repressor / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / Translation regulation / tRNA-binding / Acetylation / Methylation / Antibiotic resistance / Transcription / Transcription regulation / Transcription termination / Phosphoprotein

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