› 3n9p

X-ray diffraction
2.39Å resolution

ceKDM7A from C.elegans, complex with H3K4me3K27me2 peptide and NOG

Released:
DOI: 10.2210/pdb3n9p/pdb
PDB entry 3n9p coloured by chain, front view.
PDB entry 3n9p coloured by chain, side view.
PDB entry 3n9p coloured by chain, top view.
Source organism: Caenorhabditis elegans
Primary publication:
Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans.
Yang Y, Hu L, Wang P, Hou H, Lin Y, Liu Y, Li Z, Gong R, Feng X, Zhou L, Zhang W, Dong Y, Yang H, Lin H, Wang Y, Chen CD, Xu Y
Cell Res 20 886-98 (2010)
PMID: 20567261

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140417 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 7 homolog Chain: A
Molecule details ›
Chain: A
Length: 528 amino acids
Theoretical weight: 61.95 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9GYI0 (Residues: 201-724; Coverage: 58%)
Gene names: F29B9.2, jmjd-1.2
Sequence domains:
Structure domains:
Histone H3 Chains: B, C
Molecule details ›
Chains: B, C
Length: 32 amino acids
Theoretical weight: 3.4 KDa
Source organism: Caenorhabditis elegans
Expression system: Not provided
UniProt:
  • Canonical: P08898 (Residues: 2-33; Coverage: 24%)
Gene names: B0035.10, F07B7.5, F08G2.3, F17E9.10, F22B3.2, F45F2.13, F54E12.1, F55G1.2, K06C4.13, K06C4.5, T10C6.13, ZK131.2, ZK131.3, ZK131.7, his-13, his-17, his-2, his-25, his-27, his-32, his-42, his-45, his-49, his-55, his-59, his-6, his-63, his-9

Ligands and Environments

3 bound ligands:
Ligand FE2 1 x FE2
Ligand ZN 2 x ZN
Ligand OGA 1 x OGA
2 modified residues:
Ligand M3L 2 x M3L
Ligand MLY 2 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 60.112Å b: 86.368Å c: 62.744Å
α: 90° β: 113.18° γ: 90°
R-values:
R R work R free
0.202 0.2 0.242
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Molecular mechanisms and potential functions of histone demethylases.
Kooistra et al. (2012)
8 more

4 mentions without citation

Structural and functional coordination of DNA and histone methylation.
Cheng X. (2014)
3 more