Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.16 kDa 
• Atom Count: 1728 
• Residue Count: 172 
• Unique protein chains: 2

2V89

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

• DOI: 10.2210/pdb2V89/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-08-03 Released: 2007-12-11 
• Deposition Author(s): Ramon-Maiques, S., Yang, W.

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Experimental Data Snapshot

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

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

• PubMed: 18033247 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VDJ RECOMBINATION-ACTIVATING PROTEIN 2	A, B	82	Mus musculus	Mutation(s): 0  Gene Names: Rag2, Rag-2
Find proteins for P21784 (Mus musculus) Explore P21784  Go to UniProtKB:  P21784

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3	D, E	10	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431 GTEx  ENSG00000197409GTEx  ENSG00000197153GTEx  ENSG00000278828GTEx  ENSG00000275714GTEx  ENSG00000273983GTEx  ENSG00000274750GTEx  ENSG00000275379GTEx  ENSG00000277775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	D,E	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

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 = 75.978	α = 90
b = 46.807	β = 106.78
c = 56.808	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-03 
• Released Date: 2007-12-11 
Deposition Author(s): Ramon-Maiques, S., Yang, W.

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