› 7bqz

X-ray diffraction
3.1Å resolution

Crystal Structure of Spindlin1 bound to H3(K4me3-K9me3) peptide

Released:
DOI: 10.2210/pdb7bqz/pdb
PDB entry 7bqz coloured by chain, front view.
PDB entry 7bqz coloured by chain, side view.
PDB entry 7bqz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1.
Zhao F, Liu Y, Su X, Lee JE, Song Y, Wang D, Ge K, Gao J, Zhang MQ, Li H
J Biol Chem 295 16877-16887 (2020)
PMID: 32994220

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180745 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Spindlin-1 Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 220 amino acids
Theoretical weight: 25.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y657 (Residues: 45-262; Coverage: 83%)
Gene names: OCR, SPIN, SPIN1
Sequence domains: Spin/Ssty Family
Histone H3.2 Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 15 amino acids
Theoretical weight: 1.65 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q71DI3 (Residues: 2-16; Coverage: 11%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D

Ligands and Environments

No bound ligands
1 modified residue:
Ligand M3L 8 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 40.521Å b: 142.681Å c: 132.295Å
α: 90° β: 95.39° γ: 90°
R-values:
R R work R free
0.226 0.224 0.264
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes.
Beacon et al. (2021)
1 more

2 mentions without citation

Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1.
Zhao et al. (2020)
1 more