› 4l7x

X-ray diffraction
1.35Å resolution

Crystal structure of the DIDO PHD finger in complex with H3K4me3

Released:
DOI: 10.2210/pdb4l7x/pdb
PDB entry 4l7x coloured by chain, front view.
PDB entry 4l7x coloured by chain, side view.
PDB entry 4l7x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Dido3 PHD modulates cell differentiation and division.
Gatchalian J, Fütterer A, Rothbart SB, Tong Q, Rincon-Arano H, Sánchez de Diego A, Groudine M, Strahl BD, Martínez-A C, van Wely KH, Kutateladze TG
Cell Rep 4 148-58 (2013)
PMID: 23831028

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159440 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Death-inducer obliterator 1 Chain: A
Molecule details ›
Chain: A
Length: 63 amino acids
Theoretical weight: 7.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BTC0 (Residues: 266-325; Coverage: 3%)
Gene names: C20orf158, DATF1, DIDO1, KIAA0333
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.1 Chain: U
Molecule details ›
Chain: U
Length: 12 amino acids
Theoretical weight: 1.35 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-13; Coverage: 9%)
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 M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P41212
Unit cell:
a: 40.82Å b: 40.82Å c: 80.62Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.14 0.132 0.142
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Interpreting the language of histone and DNA modifications.
Rothbart et al. (2014)
4 more

7 mentions without citation

Atypical histone targets of PHD fingers.
Black et al. (2023)
6 more