› 5fb1

X-ray diffraction
2.1Å resolution

Crystal Structure of a PHD finger bound to histone H3 K9me3 peptide

Released:
DOI: 10.2210/pdb5fb1/pdb
PDB entry 5fb1 coloured by chain, front view.
PDB entry 5fb1 coloured by chain, side view.
PDB entry 5fb1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C.
Zhang X, Zhao D, Xiong X, He Z, Li H
J Biol Chem 291 12786-12798 (2016)
PMID: 27129259

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149986 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Nuclear autoantigen Sp-100 Chain: A
Molecule details ›
Chain: A
Length: 181 amino acids
Theoretical weight: 21.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P23497 (Residues: 466-498, 499-508; Coverage: 5%)
Gene name: SP100
Structure domains:
Histone H3.1 Chain: C
Molecule details ›
Chain: C
Length: 15 amino acids
Theoretical weight: 1.57 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-16; Coverage: 11%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand MLI 1 x MLI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21212
Unit cell:
a: 52.84Å b: 102.964Å c: 44.955Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.167 0.22
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

The Speckled Protein (SP) Family: Immunity's Chromatin Readers.
Fraschilla et al. (2020)
2 more

2 mentions without citation

Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C.
Zhang et al. (2016)
1 more