› 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 entry 4jjn coloured by chain, front view.
PDB entry 4jjn coloured by chain, side view.
PDB entry 4jjn coloured by chain, top view.
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 110 8495-500 (2013)
PMID: 23650358

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117701 (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 Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae.
Gartenberg et al. (2016)
8 more

4 mentions without citation

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