3GNB | pdb_00003gnb

Crystal structure of the RAG1 nonamer-binding domain with DNA

• PDB DOI: https://doi.org/10.2210/pdb3GNB/pdb
• NAKB: 3GNB

• Classification: RECOMBINATION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-16 Released: 2009-04-28 
• Deposition Author(s): Yin, F.F., Bailey, S., Innis, C.A., Steitz, T.A., Schatz, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.267 (Depositor) 
• R-Value Work: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

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

• PubMed: 19396172 
• DOI: https://doi.org/10.1038/nsmb.1593
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.36 kDa 
• Atom Count: 1,112 
• Modeled Residue Count: 96 
• Deposited Residue Count: 124 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V(D)J recombination-activating protein 1	A	96	Mus musculus	Mutation(s): 0  Gene Names: Rag1, Rag-1 EC: 3.1 (UniProt), 2.3.2.27 (UniProt)
UniProt
Find proteins for P15919 (Mus musculus) Explore P15919  Go to UniProtKB:  P15919

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*TP*TP*TP*TP*CP*AP*GP*AP*AP*AP*CP*C)-3'	B [auth D]	14	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*GP*TP*TP*TP*CP*TP*GP*AP*AP*AP*AP*C)-3'	C [auth E]	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.267 (Depositor) 
• R-Value Work:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.47	α = 90
b = 97.47	β = 90
c = 69.78	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-28 
Deposition Author(s): Yin, F.F., Bailey, S., Innis, C.A., Steitz, T.A., Schatz, D.G.

Revision History  

• Version 1.0: 2009-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description