› 4iut

X-ray diffraction
2.7Å resolution

crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide

Released:
DOI: 10.2210/pdb4iut/pdb
PDB entry 4iut coloured by chain, front view.
PDB entry 4iut coloured by chain, side view.
PDB entry 4iut coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AM, Strahl BD, Patel DJ, Jacobsen SE
Nature 498 385-9 (2013)
PMID: 23636332

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157790 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein SAWADEE HOMEODOMAIN HOMOLOG 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 135 amino acids
Theoretical weight: 15.78 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9XI47 (Residues: 125-258; Coverage: 52%)
Gene names: At1g15215, DTF1, F9L1.16, SHH1
Sequence domains: SAWADEE domain
Structure domains:
Histone H3.1 Chain: C
Molecule details ›
Chain: C
Length: 15 amino acids
Theoretical weight: 1.59 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
UniProt:
  • Canonical: P59226 (Residues: 2-16; Coverage: 11%)
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

2 bound ligands:
Ligand ZN 2 x ZN
Ligand CVM 2 x CVM
1 modified residue:
Ligand MLY 1 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 53.391Å b: 56.706Å c: 59.057Å
α: 90° β: 93.22° γ: 90°
R-values:
R R work R free
0.204 0.202 0.248
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

52 review citations

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.
Matzke et al. (2014)
51 more

10 mentions without citation

DNA methylation pathways and their crosstalk with histone methylation.
Du et al. (2015)
9 more