4V7I

Ribosome-SecY complex.

This is a non-PDB format compatible entry.

Summary for 4V7I

• Entry DOI: 10.2210/pdb4v7i/pdb
• Related: 3BO0 3BO1 3KC4
• EMDB information: 1484
• Descriptor: 5S ribosomal RNA, 50S ribosomal protein L5, 50S ribosomal protein L6, ... (56 entities in total)
• Functional Keywords: 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, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 56
• Total formula weight: 2233344.03

Authors

Gumbart, J.C.,Trabuco, L.G.,Schreiner, E.,Villa, E.,Schulten, K. (deposition date: 2009-10-21, release date: 2014-07-09, Last modification date: 2024-02-28)

Primary citation

Gumbart, J.,Trabuco, L.G.,Schreiner, E.,Villa, E.,Schulten, K.
Regulation of the protein-conducting channel by a bound ribosome.
Structure, 17:1453-1464, 2009

PubMed Abstract: 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.

PubMed: 19913480
DOI: 10.1016/j.str.2009.09.010

Experimental method

ELECTRON MICROSCOPY (9.6 Å)