1ID3 | pdb_00001id3

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 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.218 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1ID3

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 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. 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.

Macromolecule Content 

  • Total Structure Weight: 200.15 kDa 
  • Atom Count: 12,124 
  • Modeled Residue Count: 1,057 
  • Deposited Residue Count: 1,288 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence 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))
Explore P61830 
Go to UniProtKB:  P61830
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61830
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence 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))
Explore P02309 
Go to UniProtKB:  P02309
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02309
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence 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))
Explore P04911 
Go to UniProtKB:  P04911
Entity Groups
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UniProt GroupP04911
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence 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
Entity Groups
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UniProt GroupP02294
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
PALINDROMIC 146BP DNA FRAGMENTA [auth I],
B [auth J]
146Homo sapiens
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN

Query on MN



Download:Ideal Coordinates CCD File
AA [auth H]
K [auth I]
L [auth I]
M [auth I]
N [auth I]
AA [auth H],
K [auth I],
L [auth I],
M [auth I],
N [auth I],
O [auth J],
P [auth J],
Q [auth J],
R [auth J],
S [auth J],
T [auth J],
U [auth J],
V [auth C],
W [auth C],
X [auth D],
Y [auth E],
Z [auth G]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.292 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.218 (DCC) 
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