› 4ld9

X-ray diffraction
3.31Å resolution

Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle

Released:
DOI: 10.2210/pdb4ld9/pdb
PDB entry 4ld9 coloured by chain, front view.
PDB entry 4ld9 coloured by chain, side view.
PDB entry 4ld9 coloured by chain, top view.
Source organisms:
Primary publication:
The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle.
Arnaudo N, Fernández IS, McLaughlin SH, Peak-Chew SY, Rhodes D, Martino F
Nat Struct Mol Biol 20 1119-21 (2013)
PMID: 23934150

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-117783 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
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
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.97 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
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: 236 amino acids
Theoretical weight: 28.07 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P06701 (Residues: 2-229; Coverage: 23%)
Gene names: CMT1, L9753.10, MAR2, SIR3, STE8, YLR442C
Sequence domains: BAH domain
Structure domains: SH3 type barrels.
Widom 601 sequence reverse Chain: I
Molecule details ›
Chain: I
Length: 167 nucleotides
Theoretical weight: 51.81 KDa
Widom 601 sequence forward Chain: J
Molecule details ›
Chain: J
Length: 167 nucleotides
Theoretical weight: 51.34 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P61
Unit cell:
a: 105.513Å b: 105.513Å c: 488.225Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.24 0.238 0.295
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda

Quick links

Citations

17 review citations

Nucleosome structure and function.
McGinty et al. (2015)
16 more

4 mentions without citation

Touch, act and go: landing and operating on nucleosomes.
Speranzini et al. (2016)
3 more