› 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 1id3 coloured by chain and viewed from the front.
PDB 1id3 coloured by chain and viewed from the side.
PDB 1id3 coloured by chain and viewed from the top.
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)
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

46 review citations

Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological Implication.
Nothof et al. (2022)
45 more

88 mentions without citation

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