4V6P

Structural characterization of mRNA-tRNA translocation intermediates (class 4b of the six classes)

This is a non-PDB format compatible entry.

Summary for 4V6P

• Entry DOI: 10.2210/pdb4v6p/pdb
• Related: 2I2U 2I2V 3J0T 3J0U 3J0V 3J0W 3J0Z 3J10 3J11 3J12 3J13 3J14
• EMDB information: 5359 5360 5361 5362 5363 5364
• Descriptor: 16S ribosomal RNA, 30S ribosomal protein S7, 30S ribosomal protein S8, ... (60 entities in total)
• Functional Keywords: cryoelectron microscopy, molecular dynamics flexible fitting, ratchet-like rotation, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 58
• Total formula weight: 2258696.06

Authors

Agirrezabala, X.,Liao, H.,Schreiner, E.,Fu, J.,Ortiz-Meoz, R.F.,Schulten, K.,Green, R.,Frank, J. (deposition date: 2011-12-08, release date: 2014-07-09, Last modification date: 2025-03-19)

Primary citation

Agirrezabala, X.,Liao, H.Y.,Schreiner, E.,Fu, J.,Ortiz-Meoz, R.F.,Schulten, K.,Green, R.,Frank, J.
Structural characterization of mRNA-tRNA translocation intermediates.
Proc.Natl.Acad.Sci.USA, 109:6094-6099, 2012

PubMed Abstract: 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.

PubMed: 22467828
DOI: 10.1073/pnas.1201288109

Experimental method

ELECTRON MICROSCOPY (13.5 Å)