Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.82 kDa 
• Atom Count: 4567 
• Modelled Residue Count: 576 
• Deposited Residue Count: 636 
• Unique protein chains: 2

2B3T

Structure of complex between E. coli translation termination factor RF1 and the PrmC methyltransferase

• PDB DOI: 10.2210/pdb2B3T/pdb

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


• Deposited: 2005-09-21 Released: 2006-01-24 
• Deposition Author(s): Graille, M., Heurgue-Hamard, V., Champ, S., Mora, L., Scrima, N., Ulryck, N., van Tilbeurgh, H., Buckingham, R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.303 
• R-Value Work: 0.244 

Literature

Molecular basis for bacterial class I release factor methylation by PrmC

Graille, M., Heurgue-Hamard, V., Champ, S., Mora, L., Scrima, N., Ulryck, N., van Tilbeurgh, H., Buckingham, R.H.

(2005) Mol Cell 20: 917-927

• PubMed: 16364916 
• DOI: 10.1016/j.molcel.2005.10.025
• Primary Citation of Related Structures:  
  2B3T


• PubMed Abstract: 
  

Class I release factors bind to ribosomes in response to stop codons and trigger peptidyl-tRNA hydrolysis at the P site. Prokaryotic and eukaryotic RFs share one motif: a GGQ tripeptide positioned in a loop at the end of a stem region that interacts with the ribosomal peptidyl transferase center. The glutamine side chain of this motif is specifically methylated in both prokaryotes and eukaryotes. Methylation in E. coli is due to PrmC and results in strong stimulation of peptide chain release. We have solved the crystal structure of the complex between E. coli RF1 and PrmC bound to the methyl donor product AdoHCy. Both the GGQ domain (domain 3) and the central region (domains 2 and 4) of RF1 interact with PrmC. Structural and mutagenic data indicate a compact conformation of RF1 that is unlike its conformation when it is bound to the ribosome but is similar to the crystal structure of the protein alone.

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Organizational Affiliation: 

Institut de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS, UMR8619, Université Paris-Sud, Orsay, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein methyltransferase hemK	A	276	Escherichia coli	Mutation(s): 0  Gene Names: hemK EC: 2.1.1 (PDB Primary Data), 2.1.1.297 (UniProt)
UniProt
Find proteins for P0ACC1 (Escherichia coli (strain K12)) Explore P0ACC1  Go to UniProtKB:  P0ACC1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide chain release factor 1	B	360	Escherichia coli	Mutation(s): 0  Gene Names: prfA, sueB, uar
UniProt
Find proteins for P0A7I0 (Escherichia coli (strain K12)) Explore P0A7I0  Go to UniProtKB:  P0A7I0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.303 
• R-Value Work: 0.244 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.54	α = 90
b = 77.47	β = 90
c = 89.49	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
MOLREP	phasing
CNS	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-21 
• Released Date: 2006-01-24 
Deposition Author(s): Graille, M., Heurgue-Hamard, V., Champ, S., Mora, L., Scrima, N., Ulryck, N., van Tilbeurgh, H., Buckingham, R.H.

Revision History  

• Version 1.0: 2006-01-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-02-14
  Changes: Structure summary