1EQZ

X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


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


Literature

Asymmetries in the nucleosome core particle at 2.5 A resolution.

Harp, J.M., Hanson, B.L., Timm, D.E., Bunick, G.J.

(2000) Acta Crystallogr D Biol Crystallogr 56: 1513-1534

  • DOI: 10.1107/s0907444900011847
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The 2.5 A X-ray crystal structure of the nucleosome core particle presented here provides significant additions to the understanding of the nucleosome, the fundamental unit of chromatin structure. Extensions are made to the structure of the N-termina ...

    The 2.5 A X-ray crystal structure of the nucleosome core particle presented here provides significant additions to the understanding of the nucleosome, the fundamental unit of chromatin structure. Extensions are made to the structure of the N-terminal histone tails and details are provided on hydration and ion binding. The structure is composed of twofold symmetric molecules, native chicken histone octamer cores and the DNA palindrome, which were expected to form a perfectly twofold symmetric nucleosome core particle. In fact, the result is asymmetric owing to the binding of the DNA to the protein surface and to the packing of the particles in the crystal lattice. An analysis is made of the asymmetries by comparisons both within the nucleosome core particle and to the structure of the histone octamer core of the nucleosome.

    Related Citations: 
    • X-Ray Diffraction Analysis of Crystals Containing Two Fold Symmetric Nucleosome Core Particles
      Harp, J.M., Uberbacher, E.C., Roberson, A., Palmer, E., Gewiess, A., Bunick, G.J.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 283
    • Structural Analysis of Members of a Repeated DNA Family in Primates
      Hauser, L.J.
      (1985) Thesis --: --
    Organizational Affiliation: 

    University of Tennessee/Oak Ridge Graduate Program for Genome Sciences and Technology, Oak Ridge National Laboratory, Oak Ridge, TN 37831-8080, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HISTONE H2A)A, E129Gallus gallusMutation(s): 0 
Find proteins for P02263 (Gallus gallus)
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Go to UniProtKB:  P02263
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HISTONE H2B)B, F126Gallus gallusMutation(s): 0 
Gene Names: H2B-VII
Find proteins for P0C1H5 (Gallus gallus)
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Go to UniProtKB:  P0C1H5
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HISTONE H4)D, H103Gallus gallusMutation(s): 0 
Gene Names: H4-I, H4-II, H4-III, H4-IV, H4-V, H4-VI, H4-VII
Find proteins for P62801 (Gallus gallus)
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Go to UniProtKB:  P62801
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HISTONE H3)C, G136Gallus gallusMutation(s): 0 
Gene Names: H3-I, H3-II, H3-III, H3-IV, H3-V, H3-VI, H3-VII, H3-VIII
Find proteins for P84229 (Gallus gallus)
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Go to UniProtKB:  P84229
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
146 NUCLEOTIDES LONG DNAI, J146N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC
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G
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M		 Ligand Interaction
MN
Query on MN
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I, J
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
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I, J
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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A, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.28α = 90
b = 109.71β = 90
c = 181.12γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description