› 4jjn

X-ray diffraction
3.09Å resolution

Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome

Released:
DOI: 10.2210/pdb4jjn/pdb
PDB 4jjn coloured by chain and viewed from the front.
PDB 4jjn coloured by chain and viewed from the side.
PDB 4jjn coloured by chain and viewed from the top.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA.
Wang F, Li G, Altaf M, Lu C, Currie MA, Johnson A, Moazed D
Proc. Natl. Acad. Sci. U.S.A. (2013)
PMID: 23650358

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.26 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
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 S288C
Expression system: Escherichia coli BL21(DE3)
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.2 Chains: C, G
Molecule details ›
Chains: C, G
Length: 131 amino acids
Theoretical weight: 13.88 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04912 (Residues: 2-132; Coverage: 99%)
Gene names: H2A2, HTA2, YBL003C, YBL0103
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 S288C
Expression system: Escherichia coli BL21(DE3)
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
Regulatory protein SIR3 Chains: K, L
Molecule details ›
Chains: K, L
Length: 382 amino acids
Theoretical weight: 43.66 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06701 (Residues: 2-382; Coverage: 39%)
Gene names: CMT1, L9753.10, MAR2, SIR3, STE8, YLR442C
Sequence domains: BAH domain
Structure domains: SH3 type barrels.
DNA (146-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.14 KDa
DNA (146-MER) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.61 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P61
Unit cell:
a: 103.682Å b: 103.682Å c: 556.378Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.232 0.231 0.255
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

The regional sequestration of heterochromatin structural proteins is critical to form and maintain silent chromatin.
Oh et al. (2022)
8 more

3 mentions without citation

Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA.
Wang et al. (2013)
2 more