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 

Starting Models: experimental
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This is version 1.4 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: https://doi.org/10.1107/s0907444900011847
  • Primary Citation of Related Structures:  
    1EQZ

  • 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-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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (HISTONE H2A)C [auth A],
G [auth E]
129Gallus gallusMutation(s): 0 
UniProt
Find proteins for P02263 (Gallus gallus)
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Go to UniProtKB:  P02263
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UniProt GroupP02263
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (HISTONE H2B)D [auth B],
H [auth F]
126Gallus gallusMutation(s): 0 
UniProt
Find proteins for P0C1H5 (Gallus gallus)
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UniProt GroupP0C1H5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (HISTONE H3)E [auth C],
I [auth G]
136Gallus gallusMutation(s): 0 
UniProt
Find proteins for P84229 (Gallus gallus)
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UniProt GroupP84229
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (HISTONE H4)F [auth D],
J [auth H]
103Gallus gallusMutation(s): 0 
UniProt
Find proteins for P62801 (Gallus gallus)
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UniProt GroupP62801
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Entity ID: 1
MoleculeChains LengthOrganismImage
146 NUCLEOTIDES LONG DNAA [auth I],
B [auth J]
146N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

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IA [auth G]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
MN
Query on MN

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AA [auth J]
BA [auth J]
CA [auth J]
DA [auth J]
EA [auth J]
AA [auth J],
BA [auth J],
CA [auth J],
DA [auth J],
EA [auth J],
FA [auth J],
L [auth I],
M [auth I],
N [auth I],
O [auth I],
P [auth I],
Q [auth I],
R [auth I],
S [auth I],
T [auth I]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

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K [auth I]
U [auth J]
V [auth J]
W [auth J]
X [auth J]
K [auth I],
U [auth J],
V [auth J],
W [auth J],
X [auth J],
Y [auth J],
Z [auth J]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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GA [auth A],
HA [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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  (Full details and data files)

  • 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
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description