2V86

Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

The Plant Homeodomain Finger of Rag2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2.

Ramon-Maiques, S., Kuo, A.J., Carney, D., Matthews, A.G.W., Oettinger, M.A., Gozani, O., Yang, W.

(2007) Proc Natl Acad Sci U S A 104: 18993

  • DOI: 10.1073/pnas.0709170104
  • Primary Citation of Related Structures:  
    2V83, 2V85, 2V86, 2V87, 2V88

  • PubMed Abstract: 

    • Recombination activating gene (RAG) 1 and RAG2 together catalyze V(D)J gene rearrangement in lymphocytes as the first step in the assembly and maturation of antigen receptors. RAG2 contains a plant homeodomain (PHD) near its C terminus (RAG2-PHD) that recognizes histone H3 methylated at lysine 4 (H3K4me) and influences V(D)J recombination ...

    Recombination activating gene (RAG) 1 and RAG2 together catalyze V(D)J gene rearrangement in lymphocytes as the first step in the assembly and maturation of antigen receptors. RAG2 contains a plant homeodomain (PHD) near its C terminus (RAG2-PHD) that recognizes histone H3 methylated at lysine 4 (H3K4me) and influences V(D)J recombination. We report here crystal structures of RAG2-PHD alone and complexed with five modified H3 peptides. Two aspects of RAG2-PHD are unique. First, in the absence of the modified peptide, a peptide N-terminal to RAG2-PHD occupies the substrate-binding site, which may reflect an autoregulatory mechanism. Second, in contrast to other H3K4me3-binding PHD domains, RAG2-PHD substitutes a carboxylate that interacts with arginine 2 (R2) with a Tyr, resulting in binding to H3K4me3 that is enhanced rather than inhibited by dimethylation of R2. Five residues involved in histone H3 recognition were found mutated in severe combined immunodeficiency (SCID) patients. Disruption of the RAG2-PHD structure appears to lead to the absence of T and B lymphocytes, whereas failure to bind H3K4me3 is linked to Omenn Syndrome. This work provides a molecular basis for chromatin-dependent gene recombination and presents a single protein domain that simultaneously recognizes two distinct histone modifications, revealing added complexity in the read-out of combinatorial histone modifications.

    Related Citations: 
    • Rag2 Phd Finger Couples Histone H3 Lysine 4 Trimethylation with V(D)J Recombination.
      Matthews, A.G.W., Kuo, A.J., Ramon-Maiques, S., Han, S., Champagne, K.S., Ivanov, D., Gallardo, M., Carney, D., Cheung, P., Ciccone, D.N., Walter, K.L., Utz, P.J., Shi, Y., Kutateladze, T.G., Yang, W., Gozani, O., Oettinger, M.A.
      (2007) Nature 450: 1106
    Organizational Affiliation: 

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VDJ RECOMBINATION-ACTIVATING PROTEIN 2A, B82Mus musculusMutation(s): 0 
Gene Names: Rag2, Rag-2
UniProt
Find proteins for P21784 (Mus musculus)
Explore P21784 
Go to UniProtKB:  P21784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21784
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
H3R2ME2AK4ME3 PEPTIDEC [auth D],
D [auth E]		9Mus musculusMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P84228 (Mus musculus)
Explore P84228 
Go to UniProtKB:  P84228
Entity Groups  
UniProt GroupP84228
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DA2
Query on DA2		C [auth D],
D [auth E]		L-PEPTIDE LINKINGC8 H18 N4 O2ARG
M3L
Query on M3L		C [auth D],
D [auth E]		L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.905α = 90
b = 66.569β = 90
c = 87.495γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2013-11-06
    Changes: Atomic model, Non-polymer description, Other
  • Version 1.3: 2017-02-08
    Changes: Database references, Non-polymer description, Other, Source and taxonomy
  • Version 2.0: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other, Polymer sequence
  • Version 2.1: 2019-05-08
    Changes: Data collection, Experimental preparation