› 1id3

X-ray diffraction
3.1Å resolution

CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS

Released:
DOI: 10.2210/pdb1id3/pdb
PDB entry 1id3 coloured by chain, front view.
PDB entry 1id3 coloured by chain, side view.
PDB entry 1id3 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions.
White CL, Suto RK, Luger K
EMBO J 20 5207-18 (2001)
PMID: 11566884

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-113952 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (5 distinct):
Histone H3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.27 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P61830 (Residues: 2-136; Coverage: 99%)
Gene names: HHT1, HHT2, N2749, SIN2, YBR010W, YBR0201, YNL031C
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: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P02309 (Residues: 2-103; Coverage: 99%)
Gene names: HHF1, HHF2, N2752, YBR009C, YBR0122, YNL030W
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A.1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 131 amino acids
Theoretical weight: 13.88 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P04911 (Residues: 2-132; Coverage: 99%)
Gene names: H2A1, HTA1, SPT11, YD9934.10, YDR225W
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B.2 Chains: D, H
Molecule details ›
Chains: D, H
Length: 130 amino acids
Theoretical weight: 14.13 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P02294 (Residues: 2-131; Coverage: 99%)
Gene names: H2B2, HTB2, YBL002W, YBL0104
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
PALINDROMIC 146BP DNA FRAGMENT Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

1 bound ligand:
Ligand MN 17 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 104.922Å b: 110.398Å c: 192.617Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.223 0.292
Expression system: Escherichia coli

Quick links

Citations

49 review citations

Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects.
Richards et al. (2002)
48 more

94 mentions without citation

Histone chaperones in nucleosome assembly and human disease.
Burgess et al. (2013)
93 more