2H5E

Crystal structure of E.coli polypeptide release factor RF3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors

Gao, H.Zhou, Z.Rawat, U.Huang, C.Bouakaz, L.Wang, C.Cheng, Z.Liu, Y.Zavialov, A.Gursky, R.Sanyal, S.Ehrenberg, M.Frank, J.Song, H.

(2007) Cell 129: 929-941

  • DOI: 10.1016/j.cell.2007.03.050
  • Primary Citation of Related Structures:  2O0F

  • PubMed Abstract: 
  • During translation termination, class II release factor RF3 binds to the ribosome to promote rapid dissociation of a class I release factor (RF) in a GTP-dependent manner. We present the crystal structure of E. coli RF3*GDP, which has a three-domain ...

    During translation termination, class II release factor RF3 binds to the ribosome to promote rapid dissociation of a class I release factor (RF) in a GTP-dependent manner. We present the crystal structure of E. coli RF3*GDP, which has a three-domain architecture strikingly similar to the structure of EF-Tu*GTP. Biochemical data on RF3 mutants show that a surface region involving domains II and III is important for distinct steps in the action cycle of RF3. Furthermore, we present a cryo-electron microscopy (cryo-EM) structure of the posttermination ribosome bound with RF3 in the GTP form. Our data show that RF3*GTP binding induces large conformational changes in the ribosome, which break the interactions of the class I RF with both the decoding center and the GTPase-associated center of the ribosome, apparently leading to the release of the class I RF.


    Organizational Affiliation

    Howard Hughes Medical Institute, Health Research, Inc. at the Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor RF-3
A, B
529Escherichia coli (strain K12)Gene Names: prfC (miaD, tos)
Find proteins for P0A7I4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7I4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GDPKd: 5.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.174α = 90.00
b = 239.781β = 90.00
c = 69.677γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
CNSrefinement
HKL-2000data scaling
CNSphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-05-26 
  • Released Date: 2007-05-15 
  • Deposition Author(s): Song, H.W., Zhou, Z.H.

Revision History 

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance