› 2kgg

Solution NMR

Solution Structure of JARID1A C-terminal PHD finger

Released:
DOI: 10.2210/pdb2kgg/pdb
PDB entry 2kgg coloured by chain, ensemble of 20 models, front view.
PDB entry 2kgg coloured by chain, ensemble of 20 models, side view.
PDB entry 2kgg coloured by chain, ensemble of 20 models, top view.
Source organism: Homo sapiens
Primary publication:
Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.
Wang GG, Song J, Wang Z, Dormann HL, Casadio F, Li H, Luo JL, Patel DJ, Allis CD
Nature 459 847-51 (2009)
PMID: 19430464

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151436 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
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
UniProt:
  • Canonical: P29375 (Residues: 1609-1659; Coverage: 3%)
Gene names: JARID1A, KDM5A, RBBP2, RBP2
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Chemical shift assignment: 93%
Refinement method: simulated annealing
Expression system: Escherichia coli

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Citations

105 review citations

Cancer epigenetics: from mechanism to therapy.
Dawson et al. (2012)
104 more

4 mentions without citation

Covalent histone modifications--miswritten, misinterpreted and mis-erased in human cancers.
Chi et al. (2010)
3 more