› 2v88

X-ray diffraction
2Å resolution

Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide

Released:
DOI: 10.2210/pdb2v88/pdb
PDB entry 2v88 coloured by chain, front view.
PDB entry 2v88 coloured by chain, side view.
PDB entry 2v88 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 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, F
Molecule details ›
Chains: D, F
Length: 8 amino acids
Theoretical weight: 902 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-9; Coverage: 6%)
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
2 modified residues:
Ligand 2MR 2 x 2MR
Ligand MLY 2 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21
Unit cell:
a: 36.2Å b: 46.685Å c: 56.869Å
α: 90° β: 97.2° γ: 90°
R-values:
R R work R free
0.196 0.196 0.232
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

3 mentions without citation

Cellular consequences of arginine methylation.
Lorton et al. (2019)
2 more