PDBe 5gt0

X-ray diffraction
2.82Å resolution

Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (5 distinct):
Histone H3.1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P68431 (Residues: 2-136; Coverage: 99%)
Gene names: H3FA, H3FB, H3FC, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 2-103; Coverage: 99%)
Gene names: 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, 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-A Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96QV6 (Residues: 2-131; Coverage: 99%)
Gene names: H2AFR, HIST1H2AA
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B type 1-C/E/F/G/I Chains: D, H
Molecule details ›
Chains: D, H
Length: 125 amino acids
Theoretical weight: 13.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62807 (Residues: 2-126; Coverage: 99%)
Gene names: H2BFA, H2BFG, H2BFH, H2BFK, H2BFL, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI
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:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 99.788Å b: 108.966Å c: 170.951Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.21 0.28
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli