2V89

Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.155 
  • R-Value Observed: 0.123 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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

  • DOI: 10.1038/nature06431
  • Primary Citation of Related Structures:  
    2V89

  • PubMed Abstract: 
  • Nuclear processes such as transcription, DNA replication and recombination are dynamically regulated by chromatin structure. Eukaryotic transcription is known to be regulated by chromatin-associated proteins containing conserved protein domains that specifically recognize distinct covalent post-translational modifications on histones ...

    Nuclear processes such as transcription, DNA replication and recombination are dynamically regulated by chromatin structure. Eukaryotic transcription is known to be regulated by chromatin-associated proteins containing conserved protein domains that specifically recognize distinct covalent post-translational modifications on histones. However, it has been unclear whether similar mechanisms are involved in mammalian DNA recombination. Here we show that RAG2--an essential component of the RAG1/2 V(D)J recombinase, which mediates antigen-receptor gene assembly--contains a plant homeodomain (PHD) finger that specifically recognizes histone H3 trimethylated at lysine 4 (H3K4me3). The high-resolution crystal structure of the mouse RAG2 PHD finger bound to H3K4me3 reveals the molecular basis of H3K4me3-recognition by RAG2. Mutations that abrogate RAG2's recognition of H3K4me3 severely impair V(D)J recombination in vivo. Reducing the level of H3K4me3 similarly leads to a decrease in V(D)J recombination in vivo. Notably, a conserved tryptophan residue (W453) that constitutes a key structural component of the K4me3-binding surface and is essential for RAG2's recognition of H3K4me3 is mutated in patients with immunodeficiency syndromes. Together, our results identify a new function for histone methylation in mammalian DNA recombination. Furthermore, our results provide the first evidence indicating that disrupting the read-out of histone modifications can cause an inherited human disease.


    Related Citations: 
    • 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

    Organizational Affiliation

    Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VDJ RECOMBINATION-ACTIVATING PROTEIN 2A, B82Mus musculusMutation(s): 0 
Gene Names: Rag2Rag-2
UniProt
Find proteins for P21784 (Mus musculus)
Explore P21784 
Go to UniProtKB:  P21784
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H3C [auth D], D [auth E]10Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
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: 1.10 Å
  • R-Value Free: 0.155 
  • R-Value Observed: 0.123 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.978α = 90
b = 46.807β = 106.78
c = 56.808γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
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: 2013-03-13
    Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2016-12-28
    Changes: Database references, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation