› 5x7x

X-ray diffraction
2.18Å resolution

The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution

Released:
DOI: 10.2210/pdb5x7x/pdb
PDB entry 5x7x coloured by chain, front view.
PDB entry 5x7x coloured by chain, side view.
PDB entry 5x7x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8.
Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y, Kurumizaka H
Biochemistry 56 2184-2196 (2017)
PMID: 28374988

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119382 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (5 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 BL21(DE3)
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 Chains: C, G
Molecule details ›
Chains: C, G
Length: 133 amino acids
Theoretical weight: 14.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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 BL21(DE3)
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
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 13 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 98.887Å b: 107.509Å c: 167.415Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.226 0.256
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

4 review citations

Histone variants at a glance.
Talbert et al. (2021)
3 more

4 mentions without citation

Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations.
Liu et al. (2021)
3 more