1T1M

Binding position of ribosome recycling factor (RRF) on the E. coli 70S ribosome

PDB DOI: https://doi.org/10.2210/pdb1T1M/pdb
NAKB: 1T1M
EM Map EMD-1077: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Escherichia coli
Mutation(s): No

Deposited: 2004-04-16 Released: 2004-06-15
Deposition Author(s): Agrawal, R.K., Sharma, M.R., Kiel, M.C., Hirokawa, G., Booth, T.M., Spahn, C.M., Grassucci, R.A., Kaji, A., Frank, J.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 12.0 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: Functional implications

Agrawal, R.K., Sharma, M.R., Kiel, M.C., Hirokawa, G., Booth, T.M., Spahn, C.M., Grassucci, R.A., Kaji, A., Frank, J.

(2004) Proc Natl Acad Sci U S A 101: 8900-8905

PubMed: 15178758 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.0401904101
Primary Citation of Related Structures:
1T1M, 1T1O

PubMed Abstract:

After the termination step of protein synthesis, a deacylated tRNA and mRNA remain associated with the ribosome. The ribosome-recycling factor (RRF), together with elongation factor G (EF-G), disassembles this posttermination complex into mRNA, tRNA, and the ribosome. We have obtained a three-dimensional cryo-electron microscopic map of a complex of the Escherichia coli 70S ribosome and RRF. We find that RRF interacts mainly with the segments of the large ribosomal subunit's (50S) rRNA helices that are involved in the formation of two central intersubunit bridges, B2a and B3. The binding of RRF induces considerable conformational changes in some of the functional domains of the ribosome. As compared to its binding position derived previously by hydroxyl radical probing study, we find that RRF binds further inside the intersubunit space of the ribosome such that the tip of its domain I is shifted (by approximately 13 A) toward protein L5 within the central protuberance of the 50S subunit, and domain II is oriented more toward the small ribosomal subunit (30S). Overlapping binding sites of RRF, EF-G, and the P-site tRNA suggest that the binding of EF-G would trigger the removal of deacylated tRNA from the P site by moving RRF toward the ribosomal E site, and subsequent removal of mRNA may be induced by a shift in the position of 16S rRNA helix 44, which harbors part of the mRNA.

Related Citations:

High resolution structure of the large ribosomal subunit from a mesophilic eubacterium
Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., Yonath, A.
(2001) Cell 107: 679

Structure of the 30S ribosomal subunit
Wimberly, B.T., Brodersen, D.E., Clemons Jr., W.M., Morgan-Warren, R.J., Carter, A.P., Vonrhein, C., Hartsch, T., Ramakrishnan, V.
(2000) Nature 407: 327

Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic
Selmer, M., Al-Karadaghi, S., Hirokawa, G., Kaji, A., Liljas, A.
(1999) Science 286: 2349

Crystal structure of the ribosome recycling factor from Escherichia coli
Kim, K.K., Min, K., Suh, S.W.
(2000) EMBO J 19: 2362

Organizational Affiliation:

Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA. agrawal@wadsworth.org

Macromolecule Content

Total Structure Weight: 38.98 kDa
Atom Count: 238
Modelled Residue Count: 238
Deposited Residue Count: 239
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosome recycling factor	C	185	Escherichia coli	Mutation(s): 0 Gene Names: frr
UniProt
Find proteins for P84154 (Escherichia coli) Explore P84154 Go to UniProtKB: P84154
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84154
Protein Feature View Expand
Reference Sequence