2V89

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.155 

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
  • Also Cited By: 2V88, 2V87, 2V86, 2V85, 2V83

  • 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.USA 104: 18993


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VDJ RECOMBINATION-ACTIVATING PROTEIN 2
A, B
82Mus musculusMutation(s): 0 
Gene Names: Rag2 (Rag-2)
Find proteins for P21784 (Mus musculus)
Go to UniProtKB:  P21784
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3
D, E
10Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
D, E
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.978α = 90.00
b = 46.807β = 106.78
c = 56.808γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHELXL-97refinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2013-03-13
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2016-12-28
    Type: Database references, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2019-03-06
    Type: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-05-08
    Type: Data collection, Experimental preparation