› 1s32

X-ray diffraction
2.05Å resolution

Molecular Recognition of the Nucleosomal 'Supergroove'

Released:
DOI: 10.2210/pdb1s32/pdb
PDB 1s32 coloured by chain and viewed from the front.
PDB 1s32 coloured by chain and viewed from the side.
PDB 1s32 coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
Molecular recognition of the nucleosomal "supergroove".
Edayathumangalam RS, Weyermann P, Gottesfeld JM, Dervan PB, Luger K
Proc Natl Acad Sci U S A 101 6864-9 (2004)
PMID: 15100411

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (5 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
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: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 119 amino acids
Theoretical weight: 12.94 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-120; Coverage: 92%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 122 amino acids
Theoretical weight: 13.52 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
palindromic alpha-satellite 146 bp DNA fragment Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

8 bound ligands:
Ligand MN 14 x MN
Ligand IMT 4 x IMT
Ligand PYB 12 x PYB
Ligand ABU 2 x ABU
Ligand BAL 2 x BAL
Ligand DIB 2 x DIB
Ligand OGG 1 x OGG
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 105.352Å b: 109.717Å c: 181.827Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.219 0.243
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Picking a nucleosome lock: Sequence- and structure-specific recognition of the nucleosome.
Makowski et al. (2020)
9 more

12 mentions without citation

Histone structure and nucleosome stability.
Mariño-Ramírez et al. (2005)
11 more