› 2v89

X-ray diffraction
1.1Å resolution

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

Released:
DOI: 10.2210/pdb2v89/pdb
PDB entry 2v89 coloured by chain, front view.
PDB entry 2v89 coloured by chain, side view.
PDB entry 2v89 coloured by chain, top view.
Source organisms:
Primary publication:
RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination.
Matthews AG, Kuo AJ, Ramón-Maiques S, Han S, Champagne KS, Ivanov D, Gallardo M, Carney D, Cheung P, Ciccone DN, Walter KL, Utz PJ, Shi Y, Kutateladze TG, Yang W, Gozani O, Oettinger MA
Nature 450 1106-10 (2007)
PMID: 18033247

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149419 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
V(D)J recombination-activating protein 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 82 amino acids
Theoretical weight: 9.36 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21784 (Residues: 414-487; Coverage: 14%)
Gene names: Rag-2, Rag2
Sequence domains: RAG2 PHD domain
Structure domains: Rag2 PHD finger
Histone H3.1 Chains: D, E
Molecule details ›
Chains: D, E
Length: 10 amino acids
Theoretical weight: 1.09 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-11; Coverage: 7%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
1 modified residue:
Ligand M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 75.978Å b: 46.807Å c: 56.808Å
α: 90° β: 106.78° γ: 90°
R-values:
R R work R free
0.123 not available 0.155
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

126 review citations

Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications.
Polo et al. (2011)
125 more

8 mentions without citation

PHD fingers: epigenetic effectors and potential drug targets.
Musselman et al. (2009)
7 more