› 2v83

X-ray diffraction
2.4Å resolution

Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide

Released:
DOI: 10.2210/pdb2v83/pdb
PDB entry 2v83 coloured by chain, front view.
PDB entry 2v83 coloured by chain, side view.
PDB entry 2v83 coloured by chain, top view.
Source organisms:
Primary publication:
The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2.
Ramón-Maiques S, Kuo AJ, Carney D, Matthews AG, Oettinger MA, Gozani O, Yang W
Proc Natl Acad Sci U S A 104 18993-8 (2007)
PMID: 18025461

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149421 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
V(D)J recombination-activating protein 2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
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: 9 amino acids
Theoretical weight: 1.11 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-10; 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 6 x ZN
1 modified residue:
Ligand M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200, APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 54.783Å b: 46.835Å c: 56.963Å
α: 90° β: 101.46° γ: 90°
R-values:
R R work R free
0.196 0.196 0.23
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

59 review citations

Protein arginine methylation in mammals: who, what, and why.
Bedford et al. (2009)
58 more

5 mentions without citation

The PHD finger: a versatile epigenome reader.
Sanchez et al. (2011)
4 more