Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Macromolecule Content

• Total Structure Weight: 21.13 kDa 
• Atom Count: 1794 
• Residue Count: 182 
• Unique protein chains: 2

2V86

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

• DOI: 10.2210/pdb2V86/pdb

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


• Deposited: 2007-08-02 Released: 2007-12-11 
• Deposition Author(s): Ramon-Maiques, S., Yang, W.

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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 

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

• PubMed: 18025461 
• DOI: 10.1073/pnas.0709170104
• Structures With Same Primary Citation


• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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
H3R2ME2AK4ME3 PEPTIDE	D, E	9	Mus musculus	Mutation(s): 0  Gene Names:  H3c2, H3-53, H3.2, H3b, Hist1h3b, H3c3, H3-143, Hist1h3c, H3c4, H3-B, Hist1h3d, H3c6, H3-F, Hist1h3e, H3c7, H3.2-221, H3f, Hist1h3f, H3c13, H3.2-616, Hist2h3b, H3c14, H3.2-615, Hist2h3c1, Hist2h3ca1, H3c15, H3.2-614, Hist2h3c2, Hist2h3ca2
Find proteins for P84228 (Mus musculus) Explore P84228  Go to UniProtKB:  P84228

Small Molecules

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

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DA2	D,E	L-PEPTIDE LINKING	C8 H18 N4 O2		ARG
M3L	D,E	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

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 = 62.905	α = 90
b = 66.569	β = 90
c = 87.495	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-02 
• 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: 2013-09-04
  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