› 3m5a

X-ray diffraction
1.75Å resolution

SET7/9 Y245A in complex with TAF10-K189me3 peptide and AdoHcy

Released:
DOI: 10.2210/pdb3m5a/pdb
PDB entry 3m5a coloured by chain, front view.
PDB entry 3m5a coloured by chain, side view.
PDB entry 3m5a coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation.
Del Rizzo PA, Couture JF, Dirk LM, Strunk BS, Roiko MS, Brunzelle JS, Houtz RL, Trievel RC
J Biol Chem 285 31849-58 (2010)
PMID: 20675860

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171459 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase SETD7 Chain: A
Molecule details ›
Chain: A
Length: 261 amino acids
Theoretical weight: 28.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8WTS6 (Residues: 110-366; Coverage: 70%)
Gene names: KIAA1717, KMT7, SET7, SET9, SETD7
Sequence domains:
Structure domains:
Transcription initiation factor TFIID subunit 10 Chain: B
Molecule details ›
Chain: B
Length: 11 amino acids
Theoretical weight: 1.3 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q12962 (Residues: 186-195; Coverage: 5%)
Gene names: TAF10, TAF2A, TAF2H, TAFII30

Ligands and Environments

3 bound ligands:
Ligand SAH 1 x SAH
Ligand CO 7 x CO
Ligand GOL 3 x GOL
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P3221
Unit cell:
a: 83.108Å b: 83.108Å c: 95.57Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.196 0.21
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Carbon-oxygen hydrogen bonding in biological structure and function.
Horowitz et al. (2012)
4 more

5 mentions without citation

Histone lysine methylation dynamics: establishment, regulation, and biological impact.
Black et al. (2012)
4 more