› 2mny

Solution NMR

NMR Structure of KDM5B PHD1 finger

Released:
DOI: 10.2210/pdb2mny/pdb
PDB entry 2mny coloured by chain, ensemble of 20 models, front view.
PDB entry 2mny coloured by chain, ensemble of 20 models, side view.
PDB entry 2mny coloured by chain, ensemble of 20 models, top view.
Source organism: Homo sapiens
Primary publication:
The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B.
Zhang Y, Yang H, Guo X, Rong N, Song Y, Xu Y, Lan W, Zhang X, Liu M, Xu Y, Cao C
Protein Cell 5 837-50 (2014)
PMID: 24952722

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-193714 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 5B Chain: A
Molecule details ›
Chain: A
Length: 55 amino acids
Theoretical weight: 6.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGL1 (Residues: 306-360; Coverage: 4%)
Gene names: JARID1B, KDM5B, PLU1, RBBP2H1
Sequence domains: PHD-finger
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: 77%
Refinement method: simulated annealing
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Histone demethylases in chromatin biology and beyond.
Dimitrova et al. (2015)
13 more