4LD9 image
Deposition Date 2013-06-24
Release Date 2013-08-14
Last Version Date 2024-11-20
Entry Detail
PDB ID:
4LD9
Keywords:
NUCLEAR PROTEIN/TRANSCRIPTION/DNA
Title:
Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle
Biological Source:
Source Organism:
Xenopus laevis (Taxon ID: 8355)
Saccharomyces cerevisiae (Taxon ID: 559292)
(Taxon ID: )
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.31 Å
R-Value Free:
0.29
R-Value Work:
0.23
R-Value Observed:
0.24
Space Group:
P 61
4LD9 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:A, E
Chain Length:136
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P84233 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:B, F
Chain Length:103
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P62799 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A
Chain IDs:C, G
Chain Length:130
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P06897 Pfam ID:PF00125, PF16211
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:D, H
Chain Length:126
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P02281 Pfam ID:PF00125
Polymer Type:polydeoxyribonucleotide
Molecule:Widom 601 sequence reverse
Chain IDs:I
Chain Length:167
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:Widom 601 sequence forward
Chain IDs:J
Chain Length:167
Number of Molecules:1
Biological Source:
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Regulatory protein SIR3
Gene (Uniprot):SIR3
Chain IDs:K, L
Chain Length:236
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06701 Pfam ID:PF01426
Ligand Molecules
NA
Primary Citation
The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle.
Nat.Struct.Mol.Biol. 20 1119 1121 (2013)
PMID: 23934150 DOI: 10.1038/nsmb.2641

Abstact

The N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown. The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome. Additionally, we present a new method for the production of protein-nucleosome complexes for structural analysis.

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Disease

Primary Citation of related structures
4LD9