› 5c11

X-ray diffraction
2.8Å resolution

Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide

Released:
DOI: 10.2210/pdb5c11/pdb
PDB entry 5c11 coloured by chain, front view.
PDB entry 5c11 coloured by chain, side view.
PDB entry 5c11 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide
Huang J, Li H
Nat Commun (2015)

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151437 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 5A Chain: A
Molecule details ›
Chain: A
Length: 52 amino acids
Theoretical weight: 5.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P29375 (Residues: 1609-1659; Coverage: 3%)
Gene names: JARID1A, KDM5A, RBBP2, RBP2
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.1 Chain: B
Molecule details ›
Chain: B
Length: 10 amino acids
Theoretical weight: 1.19 KDa
Source organism: synthetic construct
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 2 x ZN
1 modified residue:
Ligand 4WQ 1 x 4WQ

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: I432
Unit cell:
a: 108.91Å b: 108.91Å c: 108.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.246 0.279
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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