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 ...

    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 2AB82Mus musculusMutation(s): 0 
Gene Names: Rag2Rag-2
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 H3DE10Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
D,EL-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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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