3GNA

Crystal structure of the RAG1 nonamer-binding domain with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

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:  
    3GNA, 3GNB

  • 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 mechanistic studies of this reaction ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V(D)J recombination-activating protein 1A96Mus musculusMutation(s): 0 
Gene Names: Rag1Rag-1
EC: 3.1 (UniProt), 2.3.2.27 (UniProt)
UniProt
Find proteins for P15919 (Mus musculus)
Explore P15919 
Go to UniProtKB:  P15919
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15919
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*AP*CP*TP*TP*AP*AP*CP*AP*AP*AP*AP*AP*CP*C)-3'B [auth D]14N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*TP*GP*GP*TP*TP*TP*TP*TP*GP*TP*TP*AP*AP*G)-3'C [auth E]14N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.47α = 90
b = 97.47β = 90
c = 69.78γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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