4WWX

Crystal structure of the core RAG1/2 recombinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2001 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the V(D)J recombinase RAG1-RAG2.

Kim, M.S.Lapkouski, M.Yang, W.Gellert, M.

(2015) Nature 518: 507-511

  • DOI: 10.1038/nature14174

  • PubMed Abstract: 
  • V(D)J recombination in the vertebrate immune system generates a highly diverse population of immunoglobulins and T-cell receptors by combinatorial joining of segments of coding DNA. The RAG1-RAG2 protein complex initiates this site-specific recombina ...

    V(D)J recombination in the vertebrate immune system generates a highly diverse population of immunoglobulins and T-cell receptors by combinatorial joining of segments of coding DNA. The RAG1-RAG2 protein complex initiates this site-specific recombination by cutting DNA at specific sites flanking the coding segments. Here we report the crystal structure of the mouse RAG1-RAG2 complex at 3.2 Å resolution. The 230-kilodalton RAG1-RAG2 heterotetramer is 'Y-shaped', with the amino-terminal domains of the two RAG1 chains forming an intertwined stalk. Each RAG1-RAG2 heterodimer composes one arm of the 'Y', with the active site in the middle and RAG2 at its tip. The RAG1-RAG2 structure rationalizes more than 60 mutations identified in immunodeficient patients, as well as a large body of genetic and biochemical data. The architectural similarity between RAG1 and the hairpin-forming transposases Hermes and Tn5 suggests the evolutionary conservation of these DNA rearrangements.


    Organizational Affiliation

    Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, Maryland 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V(D)J recombination-activating protein 1
B, E
618Mus musculusMutation(s): 0 
Gene Names: Rag1
Find proteins for P15919 (Mus musculus)
Go to UniProtKB:  P15919
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V(D)J recombination-activating protein 2
X, Y
349Mus musculusMutation(s): 0 
Gene Names: Rag2 (Rag-2)
Find proteins for P21784 (Mus musculus)
Go to UniProtKB:  P21784
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2001 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 168.760α = 90.00
b = 180.050β = 90.00
c = 200.190γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-04
    Type: Database references
  • Version 1.2: 2015-03-11
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Data collection, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.4: 2017-11-22
    Type: Refinement description