3GNB

Crystal structure of the RAG1 nonamer-binding domain with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis.

Yin, F.F.Bailey, S.Innis, C.A.Ciubotaru, M.Kamtekar, S.Steitz, T.A.Schatz, D.G.

(2009) Nat.Struct.Mol.Biol. 16: 499-508

  • DOI: 10.1038/nsmb.1593
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The products of recombination-activating genes RAG1 and RAG2 mediate the assembly of antigen receptor genes during lymphocyte development in a process known as V(D)J recombination. Lack of structural information for the RAG proteins has hindered mech ...

    The products of recombination-activating genes RAG1 and RAG2 mediate the assembly of antigen receptor genes during lymphocyte development in a process known as V(D)J recombination. Lack of structural information for the RAG proteins has hindered mechanistic studies of this reaction. We report here the crystal structure of an essential DNA binding domain of the RAG1 catalytic core bound to its nonamer DNA recognition motif. The RAG1 nonamer binding domain (NBD) forms a tightly interwoven dimer that binds and synapses two nonamer elements, with each NBD making contact with both DNA molecules. Biochemical and biophysical experiments confirm that the two nonamers are in close proximity in the RAG1/2-DNA synaptic complex and demonstrate the functional importance of the protein-DNA contacts revealed in the structure. These findings reveal a previously unsuspected function for the NBD in DNA synapsis and have implications for the regulation of DNA binding and cleavage by RAG1 and RAG2.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V(D)J recombination-activating protein 1
A
96Mus musculusMutation(s): 0 
Gene Names: Rag1
Find proteins for P15919 (Mus musculus)
Go to UniProtKB:  P15919
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*TP*TP*TP*TP*CP*AP*GP*AP*AP*AP*CP*C)-3'D14N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*GP*GP*TP*TP*TP*CP*TP*GP*AP*AP*AP*AP*C)-3'E14N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.242 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 97.470α = 90.00
b = 97.470β = 90.00
c = 69.780γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
REFMACphasing
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance