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CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS
DOI:10.2210/pdb1id3/pdb   NDB ID: PD0209
1ID3
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Structural Protein/dna
    Structure Weight: 200151.74
    Molecule: PALINDROMIC 146BP DNA FRAGMENT
    Polymer: 1 Type: dna Length: 146
    Chains: I, J
    Organism: Homo sapiens
    Molecule: HISTONE H3
    Polymer: 2 Type: protein Length: 135
    Chains: A, E
    Organism: Saccharomyces cerevisiae
    Gene Names: HHT1 YBR010W YBR0201 HHT2 SIN2 YNL031C N2749
    UniProtKB: Protein Feature View | Search PDB | P61830  
    Molecule: HISTONE H4
    Polymer: 3 Type: protein Length: 102
    Chains: B, F
    Organism: Saccharomyces cerevisiae
    Gene Names: HHF1 YBR009C YBR0122 HHF2 YNL030W N2752
    UniProtKB: Protein Feature View | Search PDB | P02309  
    Molecule: HISTONE H2A.1
    Polymer: 4 Type: protein Length: 131
    Chains: C, G
    Organism: Saccharomyces cerevisiae
    Gene Names: HTA1 H2A1 SPT11 YDR225W YD9934.10
    UniProtKB: Protein Feature View | Search PDB | P04911  
    Molecule: HISTONE H2B.2
    Polymer: 5 Type: protein Length: 130
    Chains: D, H
    Organism: Saccharomyces cerevisiae
    Gene Names: HTB2 H2B2 YBL002W YBL0104
    UniProtKB: Protein Feature View | Search PDB | P02294  
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human 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  
     
  •   Related PDB Entries Hide
    Identifier Details
    1AOI  X-ray Structure of the Nucleosome Core Particle at 2.8A 
    1EQZ  X-ray Structure of the Nucleosome Core Particle at 2.5A Resolution 
    1F66  2.6A Crystal Structure of a Nucleosome Core Particle Containing the Variant Histone H2A.Z 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MN
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    MN Mn
    MANGANESE (II) ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: PD0209
     
 
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:   White, C.L.,  Suto, R.K.,  Luger, K.

    Deposition:   2001-04-03
    Release:   2001-09-28
    Last Modified (REVDAT):   2009-02-24
     
  •   Revision History    Hide
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    2011-07-13
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  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   3.10
    R-Value: 0.223 (work)
    R-Free: 0.292
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 104.92 α = 90.00 
    b = 110.40 β = 90.00 
    c = 192.62 γ = 90.00