2H5E

Crystal structure of E.coli polypeptide release factor RF3

• PDB DOI:  https://doi.org/10.2210/pdb2H5E/pdb

• Classification: TRANSLATION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.225 

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

• PubMed: 17540173 
• DOI: https://doi.org/10.1016/j.cell.2007.03.050
• Primary Citation of Related Structures:  
  2H5E, 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 120.19 kDa 
• Atom Count: 7,810 
• Modelled Residue Count: 967 
• Deposited Residue Count: 1,058 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide chain release factor RF-3	A, B	529	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7I4 (Escherichia coli (strain K12)) Explore P0A7I4  Go to UniProtKB:  P0A7I4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], D [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GDP	PDBBind:  2H5E	Kd: 5.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.174	α = 90
b = 239.781	β = 90
c = 69.677	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
HKL-2000	data reduction
CNS	refinement
REFMAC	refinement
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance