› 5yvx

X-ray diffraction
1.59Å resolution

Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide

Released:
DOI: 10.2210/pdb5yvx/pdb
PDB entry 5yvx coloured by chain, front view.
PDB entry 5yvx coloured by chain, side view.
PDB entry 5yvx coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Uncovering the mechanistic basis for specific recognition of monomethylated H3K4 by the CW domain of Arabidopsis histone methyltransferase SDG8.
Liu Y, Huang Y
J Biol Chem 293 6470-6481 (2018)
PMID: 29496997

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157782 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase ASHH2 Chain: A
Molecule details ›
Chain: A
Length: 60 amino acids
Theoretical weight: 6.91 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q2LAE1 (Residues: 862-921; Coverage: 3%)
Gene names: ASHH2, At1g77300, EFS, LAZ2, SDG8, SET8, T14N5.15
Sequence domains: CW-type Zinc Finger
Structure domains: Herpes Virus-1
Histone H3.1 Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.08 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
UniProt:
  • Canonical: P59226 (Residues: 2-10; Coverage: 7%)
Gene names: At1g09200, At3g27360, At5g10390, At5g10400, At5g65360, F12B17_250, F12B17_260, HTR1, HTR13, HTR2, HTR3, HTR9, K1G2.8, MNA5.9, T12M4.9

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand MLZ 1 x MLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P63
Unit cell:
a: 66.421Å b: 66.421Å c: 29.241Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.169 0.168 0.184
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Reprogramming of Histone H3 Lysine Methylation During Plant Sexual Reproduction.
Fang et al. (2021)
12 other articles

2 mentions without citation

Uncovering the mechanistic basis for specific recognition of monomethylated H3K4 by the CW domain of Arabidopsis histone methyltransferase SDG8.
Liu et al. (2018)
1 more