Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A3B2C2D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 200.89 kDa 
• Atom Count: 13325 
• Modelled Residue Count: 1170 
• Deposited 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

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

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Gallus gallus
• Mutation(s): No 


• 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: 2.50 Å
• R-Value Free: 0.282 
• R-Value Work: 0.219 
• R-Value Observed: 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 D Biol Crystallogr 56: 1513-1534

• PubMed: 11092917 
• DOI: 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.

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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 --: --

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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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HISTONE H2A)	C [auth A], G [auth E]	129	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P02263 (Gallus gallus) Explore P02263  Go to UniProtKB:  P02263

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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HISTONE H3)	E [auth C], I [auth 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
UniProt
Find proteins for P84229 (Gallus gallus) Explore P84229  Go to UniProtKB:  P84229

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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
146 NUCLEOTIDES LONG DNA	A [auth I], B [auth J]	146	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	IA [auth G]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
MN	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	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	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 = 105.28	α = 90
b = 109.71	β = 90
c = 181.12	γ = 90

Software Package:

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