Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome
DOI:10.2210/pdb4jjn/pdb   NDB ID: NA2287
4JJN
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: DNA Binding Protein/dna
    Structure Weight: 287140.90
    Molecule: Histone H3
    Polymer: 1 Type: protein Length: 135
    Chains: A, E
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: HHT1 YBR010W YBR0201 HHT2 SIN2 YNL031C N2749
    UniProtKB: Protein Feature View | Search PDB | P61830  
    Molecule: Histone H4
    Polymer: 2 Type: protein Length: 102
    Chains: B, F
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: HHF1 YBR009C YBR0122 HHF2 YNL030W N2752
    UniProtKB: Protein Feature View | Search PDB | P02309  
    Molecule: Histone H2A.2
    Polymer: 3 Type: protein Length: 131
    Chains: C, G
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: HTA2 H2A2 YBL003C YBL0103
    UniProtKB: Protein Feature View | Search PDB | P04912  
    Molecule: Histone H2B.2
    Polymer: 4 Type: protein Length: 130
    Chains: D, H
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: HTB2 H2B2 YBL002W YBL0104
    UniProtKB: Protein Feature View | Search PDB | P02294  
    Molecule: Regulatory protein SIR3
    Polymer: 5 Type: protein Length: 382
    Chains: K, L
    Mutation: D205N
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: SIR3 CMT1 MAR2 STE8 YLR442C L9753.10
    UniProtKB: Protein Feature View | Search PDB | P06701  
    Molecule: DNA (146-MER)
    Polymer: 6 Type: dna Length: 147
    Chains: I
    Molecule: DNA (146-MER)
    Polymer: 7 Type: dna Length: 147
    Chains: J
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 3
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 4
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 5
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 6
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 7
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA2287
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors
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  •   Deposition Summary Hide
    Authors:   Wang, F.,  Li, G.,  Mohammed, A.,  Lu, C.,  Currie, M.,  Johnson, A.,  Moazed, D.

    Deposition:   2013-03-08
    Release:   2013-05-15
    Last Modified (REVDAT):   2013-06-19
     
  •   Revision History    Hide
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    2013-06-19
    Citation
    2013-06-05
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   3.09
    R-Value: 0.233 (obs.)
    R-Free: 0.255
    Space Group: P 61
    Unit Cell:
      Length [Å] Angles [°]
    a = 103.68 α = 90.00 
    b = 103.68 β = 90.00 
    c = 556.38 γ = 120.00