› 2f8n

X-ray diffraction
2.9Å resolution

2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes

Released:
DOI: 10.2210/pdb2f8n/pdb
PDB entry 2f8n coloured by chain, front view.
PDB entry 2f8n coloured by chain, side view.
PDB entry 2f8n coloured by chain, top view.
Source organisms:
Entry authors: Chakravarthy S, Luger K

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115241 (preferred)
Entry contents:
6 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (7 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.42 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
H2B.U histone 2 Chain: D
Molecule details ›
Chain: D
Length: 126 amino acids
Theoretical weight: 14.03 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9D2U9 (Residues: 1-126; Coverage: 100%)
Gene names: H2bu2, Hist3h2ba
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H2B 1.1 Chain: H
Molecule details ›
Chain: H
Length: 123 amino acids
Theoretical weight: 13.66 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Core histone macro-H2A.1 Chain: G
Molecule details ›
Chain: G
Length: 120 amino acids
Theoretical weight: 12.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75367 (Residues: 1-120; Coverage: 33%)
Gene names: H2AFY, MACROH2A1
Sequence domains:
Structure domains: Histone, subunit A
Histone H2A type 1-H Chain: K
Molecule details ›
Chain: K
Length: 149 amino acids
Theoretical weight: 16.2 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8CGP6 (Residues: 1-128; Coverage: 100%)
Gene names: H2ac12, Hist1h2ah
Sequence domains:
Structure domains: Histone, subunit A
alpha-satellite DNA (146 bp) Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 106.145Å b: 109.272Å c: 176.273Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.269
Expression system: Escherichia coli

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