› 5vab

X-ray diffraction
1.7Å resolution

Crystal structure of ATXR5 PHD domain in complex with histone H3

Released:
DOI: 10.2210/pdb5vab/pdb
PDB entry 5vab coloured by chain, front view.
PDB entry 5vab coloured by chain, side view.
PDB entry 5vab coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for the methylation specificity of ATXR5 for histone H3.
Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF
Nucleic Acids Res 45 6375-6387 (2017)
PMID: 28383693

Function and Biology Details

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-125019 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase ATXR6 Chain: A
Molecule details ›
Chain: A
Length: 58 amino acids
Theoretical weight: 6.23 KDa
Source organism: Glycine max
Expression system: Escherichia coli
UniProt:
  • Canonical: I1N521 (Residues: 22-75; Coverage: 16%)
Gene names: 100775247, GLYMA_18G285900
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.1 Chain: F
Molecule details ›
Chain: F
Length: 11 amino acids
Theoretical weight: 1.31 KDa
Source organism: Homo sapiens
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
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-D
Spacegroup: P4322
Unit cell:
a: 44.01Å b: 44.01Å c: 71.948Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.149 0.179
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Structure and mechanism of plant histone mark readers.
Liu et al. (2018)
2 more

2 mentions without citation

Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis.
Zhang et al. (2020)
1 more