1ID3

CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.223 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions.

White, C.L., Suto, R.K., Luger, K.

(2001) EMBO J 20: 5207-5218

  • DOI: https://doi.org/10.1093/emboj/20.18.5207
  • Primary Citation of Related Structures:  
    1ID3

  • PubMed Abstract: 

    • Chromatin is composed of nucleosomes, the universally repeating protein-DNA complex in eukaryotic cells. The crystal structure of the nucleosome core particle from Saccharomyces cerevisiae reveals that the structure and function of this fundamental complex is conserved between single-cell organisms and metazoans ...

    Chromatin is composed of nucleosomes, the universally repeating protein-DNA complex in eukaryotic cells. The crystal structure of the nucleosome core particle from Saccharomyces cerevisiae reveals that the structure and function of this fundamental complex is conserved between single-cell organisms and metazoans. Our results show that yeast nucleosomes are likely to be subtly destabilized as compared with nucleosomes from higher eukaryotes, consistent with the idea that much of the yeast genome remains constitutively open during much of its life cycle. Importantly, minor sequence variations lead to dramatic changes in the way in which nucleosomes pack against each other within the crystal lattice. This has important implications for our understanding of the formation of higher order chromatin structure and its modulation by post-translational modifications. Finally, the yeast nucleosome core particle provides a structural context by which to interpret genetic data obtained from yeast. Coordinates have been deposited with the Protein Data Bank under accession number 1ID3.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H3C [auth A],
G [auth E]		135Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HISTONE H3
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P61830
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UniProt GroupP61830
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H4D [auth B],
H [auth F]		102Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HISTONE H4
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP02309
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H2A.1E [auth C],
I [auth G]		131Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HISTONE H2A
UniProt
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP04911
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H2B.2F [auth D],
J [auth H]		130Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HISTONE H2B
UniProt
Find proteins for P02294 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02294 
Go to UniProtKB:  P02294
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UniProt GroupP02294
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Entity ID: 1
MoleculeChainsLengthOrganismImage
PALINDROMIC 146BP DNA FRAGMENTA [auth I],
B [auth J]		146Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.922α = 90
b = 110.398β = 90
c = 192.617γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description