4kud

X-ray diffraction
3.2Å resolution

Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-117764 (preferred)
Entry contents:
5 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (6 distinct):
Histone H3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.39 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P61830 (Residues: 1-136; Coverage: 100%)
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: 103 amino acids
Theoretical weight: 11.4 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P02309 (Residues: 1-103; Coverage: 100%)
Gene names: HHF1, HHF2, N2752, YBR009C, YBR0122, YNL030W
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A.2 Chains: C, G
Molecule details ›
Chains: C, G
Length: 132 amino acids
Theoretical weight: 14 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P04912 (Residues: 1-132; Coverage: 100%)
Gene names: H2A2, HTA2, YBL003C, YBL0103
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 131 amino acids
Theoretical weight: 14.28 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P02293 (Residues: 1-131; Coverage: 100%)
Gene names: H2B1, HTB1, SPT12, YD9934.09C, YDR224C
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Regulatory protein SIR3 Chains: K, L
Molecule details ›
Chains: K, L
Length: 224 amino acids
Theoretical weight: 26.77 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P06701 (Residues: 2-219; Coverage: 22%)
Gene names: CMT1, L9753.10, MAR2, SIR3, STE8, YLR442C
Sequence domains: BAH domain
Structure domains: SH3 type barrels.
nucloesome DNA Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

No bound ligands
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P61
Unit cell:
a: 108.33Å b: 108.33Å c: 498.92Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.198 0.237
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda