› 7xx5

X-ray diffraction
3.19Å resolution

Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment)

Released:
DOI: 10.2210/pdb7xx5/pdb
PDB entry 7xx5 coloured by chain, front view.
PDB entry 7xx5 coloured by chain, side view.
PDB entry 7xx5 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Adhireksan Z, Qiuye B, Lee PL, Sharma D, Padavattan S, Davey CA

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 21-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-216583 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.1 Chains: A, E, K, O
Molecule details ›
Chains: A, E, K, O
Length: 138 amino acids
Theoretical weight: 15.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P68431 (Residues: 1-136; Coverage: 100%)
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
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F, L, P
Molecule details ›
Chains: B, F, L, P
Length: 105 amino acids
Theoretical weight: 11.54 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
Histone H2A type 1-B/E Chains: C, G, M, Q
Molecule details ›
Chains: C, G, M, Q
Length: 132 amino acids
Theoretical weight: 14.31 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:
Histone H2B type 1-J Chains: D, H, N, R
Molecule details ›
Chains: D, H, N, R
Length: 128 amino acids
Theoretical weight: 14.08 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
Histone H1.3 Chain: U
Molecule details ›
Chain: U
Length: 222 amino acids
Theoretical weight: 22.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P16402 (Residues: 1-221; Coverage: 100%)
Gene names: H1-3, H1F3, HIST1H1D
Sequence domains: linker histone H1 and H5 family
DNA (169-MER) Chains: I, S
Molecule details ›
Chains: I, S
Length: 169 nucleotides
Theoretical weight: 52.17 KDa
DNA (169-MER) Chains: J, T
Molecule details ›
Chains: J, T
Length: 169 nucleotides
Theoretical weight: 52.16 KDa

Ligands and Environments

1 bound ligand:
Ligand CA 13 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 105.071Å b: 101.736Å c: 218.399Å
α: 90° β: 103.52° γ: 90°
R-values:
R R work R free
0.206 0.203 0.259
Expression system: Escherichia coli

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