2V89 | pdb_00002v89

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

• PDB DOI: https://doi.org/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 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.157 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1038/nature06431
• Primary Citation 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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Organizational Affiliation: 
• Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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: 1,728 
• Modeled Residue Count: 172 
• Deposited Residue Count: 184 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3	C [auth D], D [auth E]	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	C [auth D], D [auth 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 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.157 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

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

• 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
• Version 2.0: 2023-12-13
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description