› 5b32

X-ray diffraction
2.35Å resolution

The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3.

Released:
DOI: 10.2210/pdb5b32/pdb
PDB 5b32 coloured by chain and viewed from the front.
PDB 5b32 coloured by chain and viewed from the side.
PDB 5b32 coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A.
Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H
Open Biol 6 (2016)
PMID: 27358293

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Entry contents:
5 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (6 distinct):
Histone H3.3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 139 amino acids
Theoretical weight: 15.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P84243 (Residues: 1-136; Coverage: 100%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 106 amino acids
Theoretical weight: 11.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1-B/E Chain: C
Molecule details ›
Chain: C
Length: 133 amino acids
Theoretical weight: 14.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04908 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B type 1-J Chains: D, H
Molecule details ›
Chains: D, H
Length: 129 amino acids
Theoretical weight: 14.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06899 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H2A.Z Chain: G
Molecule details ›
Chain: G
Length: 131 amino acids
Theoretical weight: 13.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C0S5 (Residues: 1-128; Coverage: 100%)
Gene names: H2AFZ, H2AZ, H2AZ1
Sequence domains:
Structure domains: Histone, subunit A
DNA (146-MER) Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

2 bound ligands:
Ligand CL 4 x CL
Ligand MN 10 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P212121
Unit cell:
a: 98.182Å b: 105.823Å c: 166.263Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.227 0.259
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Janus Bioparticles: Asymmetric Nucleosomes and Their Preparation Using Chemical Biology Approaches.
Mitchener et al. (2021)
5 more