› 5vac

X-ray diffraction
1.95Å resolution

Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide

Released:
DOI: 10.2210/pdb5vac/pdb
PDB entry 5vac coloured by chain, front view.
PDB entry 5vac coloured by chain, side view.
PDB entry 5vac 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

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
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-110885 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Probable Histone-lysine N-methyltransferase ATXR5 Chain: A
Molecule details ›
Chain: A
Length: 229 amino acids
Theoretical weight: 26.2 KDa
Source organism: Ricinus communis
Expression system: Escherichia coli
UniProt:
  • Canonical: B9RU15 (Residues: 146-374; Coverage: 61%)
Gene names: ATXR5, RCOM_1460410
Sequence domains: SET domain
Structure domains: SET domain
Histone H3.2 Chain: C
Molecule details ›
Chain: C
Length: 19 amino acids
Theoretical weight: 1.89 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q71DI3 (Residues: 19-37; Coverage: 14%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D

Ligands and Environments

2 bound ligands:
Ligand SAH 1 x SAH
Ligand DMS 1 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: I222
Unit cell:
a: 74.548Å b: 81.353Å c: 88.503Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.189 0.228
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

1 mention without citation

Molecular basis for the methylation specificity of ATXR5 for histone H3.
Bergamin et al. (2017)