› 8qkt

X-ray diffraction
3.26Å resolution

Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment

Released:
DOI: 10.2210/pdb8qkt/pdb
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PDB entry 8qkt coloured by chain, front view.
PDB entry 8qkt coloured by chain, side view.
PDB entry 8qkt coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Ma Z, Davey CA

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-232331 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Histone H3.1 Chains: AAA, EEE, KKK, OOO
Molecule details ›
Chains: AAA, EEE, KKK, OOO
Length: 98 amino acids
Theoretical weight: 11.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P68431 (Residues: 39-136; Coverage: 72%)
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: BBB, FFF, LLL, PPP
Molecule details ›
Chains: BBB, FFF, LLL, PPP
Length: 79 amino acids
Theoretical weight: 8.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A8C1JQV0 (Residues: 14-92; Coverage: 86%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A Chains: CCC, MMM
Histone H2B type 1-J Chains: DDD, NNN
Histone H2A Chains: GGG, QQQ
Histone H2B type 1-J Chains: HHH, RRR
DNA (167-MER) Chains: III, SSS
DNA (167-MER) Chains: JJJ, TTT

Ligands and Environments

1 bound ligand:
Ligand MN 33 x MN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 108.437Å b: 103.722Å c: 185.405Å
α: 90° β: 93.59° γ: 90°
R-values:
R R work R free
0.272 0.269 0.321
Expression system: Escherichia coli

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