Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 8-mer -A4B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 200891.63 
• Atom Count: 12976 
• Residue Count: 1280 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

1EQZ

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

• DOI: 10.2210/pdb1EQZ/pdb
• NDB: PD0137

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Gallus gallus


• Deposited: 2000-04-06 Released: 2000-04-17 
• Deposition Author(s): Hanson, B.L., Harp, J.M., Timm, D.E., Bunick, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.282 
• R-Value Work: 0.219 

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.,Sect.D 56: 1513-1534

• PubMed: 11092917 


• 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.

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Related Citations: 

• Structural Analysis of Members of a Repeated DNA Family in Primates
  Hauser, L.J.
  (1985) Thesis --: --
• 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.,Sect.D 52: 283




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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

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (HISTONE H2A)	A, E	129	Gallus gallus	Mutation(s): 0
Find proteins for P02263 (Gallus gallus) Go to UniProtKB:  P02263

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (HISTONE H2B)	B, F	126	Gallus gallus	Mutation(s): 0  Gene Names: H2B-VII
Find proteins for P0C1H5 (Gallus gallus) Go to UniProtKB:  P0C1H5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (HISTONE H3)	C, G	136	Gallus gallus	Mutation(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) Go to UniProtKB:  P84229

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (HISTONE H4)	D, H	103	Gallus gallus	Mutation(s): 0  Gene Names: H4-I, H4-II, H4-III, H4-IV, H4-V, H4-VI, H4-VII
Find proteins for P62801 (Gallus gallus) Go to UniProtKB:  P62801

Entity ID: 1
Molecule	Chains	Length	Organism
146 NUCLEOTIDES LONG DNA	I,J	146	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	I, J	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MN	I, J	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	A, E	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CAC	G	CACODYLATE ION dimethylarsinate C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.282 
• R-Value Work: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 105.280	α = 90.00
b = 109.710	β = 90.00
c = 181.120	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	phasing
CCP4	model building
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-04-06 
• Released Date: 2000-04-17 
• Deposition Author(s): Hanson, B.L., Harp, J.M., Timm, D.E., Bunick, G.J.

Revision History 

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