› 4mzg

X-ray diffraction
1.7Å resolution

Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide

Released:
DOI: 10.2210/pdb4mzg/pdb
PDB entry 4mzg coloured by chain, front view.
PDB entry 4mzg coloured by chain, side view.
PDB entry 4mzg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1.
Su X, Zhu G, Ding X, Lee SY, Dou Y, Zhu B, Wu W, Li H
Genes Dev 28 622-36 (2014)
PMID: 24589551

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
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):
Histone H3.2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 20 amino acids
Theoretical weight: 2.23 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q71DI3 (Residues: 2-21; Coverage: 15%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D
Spindlin-1 Chains: B, D
Molecule details ›
Chains: B, D
Length: 222 amino acids
Theoretical weight: 25.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y657 (Residues: 50-262; Coverage: 81%)
Gene names: OCR, SPIN, SPIN1
Sequence domains: Spin/Ssty Family
Structure domains: Spindlin/Ssty

Ligands and Environments

4 bound ligands:
Ligand MRD 1 x MRD
Ligand MPD 3 x MPD
Ligand MG 1 x MG
Ligand CL 3 x CL
1 modified residue:
Ligand M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 43.168Å b: 122.037Å c: 49.837Å
α: 90° β: 91.71° γ: 90°
R-values:
R R work R free
0.184 0.183 0.207
Expression systems:
  • Not provided
  • Escherichia coli

Quick links

Citations

14 review citations

Arginine Methylation: The Coming of Age.
Blanc et al. (2017)
13 more

2 mentions without citation

Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1.
Su et al. (2014)
1 more