Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A7B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.77 kDa 
• Atom Count: 6,471 
• Modelled Residue Count: 755 
• Deposited Residue Count: 988 
• Unique protein chains: 4

 2ARO

Crystal Structure Of The Native Histone Octamer To 2.1 Angstrom Resolution, Crystalised In The Presence Of S-Nitrosoglutathione

• PDB DOI: 10.2210/pdb2ARO/pdb

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


• Deposited: 2005-08-20 Released: 2005-08-30 
• Deposition Author(s): Wood, C.M., Sodngam, S., Nicholson, J.M., Lambert, S.J., Reynolds, C.D., Baldwin, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

The oxidised histone octamer does not form a H3 disulphide bond.

Wood, C.M., Sodngam, S., Nicholson, J.M., Lambert, S.J., Reynolds, C.D., Baldwin, J.P.

(2006) Biochim Biophys Acta 1764: 1356-1362

• PubMed: 16920041 
• DOI: 10.1016/j.bbapap.2006.06.014
• Primary Citation of Related Structures:  
  2ARO


• PubMed Abstract: 
  

A H3 dimer band is produced when purified native histone octamers are run on an SDS-PAGE gel in a beta-mercaptoethanol-free environment. To investigate this, native histone octamer crystals, derived from chicken erythrocytes, and of structure (H2A-H2B)-(H4-H3)-(H3'-H4')-(H2B'-H2A'), were grown in 2 M KCl, 1.35 M potassium phosphates and 250-350 microM of the oxidising agent S-nitrosoglutathione, pH 6.9. X-ray diffraction data were acquired to 2.10 A resolution, yielding a structure with an Rwork value of 18.6% and an Rfree of 22.5%. The space group is P6(5), the asymmetric unit of which contains one complete octamer. Compared to the 1.90 A resolution, unoxidised native histone octamer structure, the crystals show a reduction of 2.5% in the c-axis of the unit cell, and free-energy calculations reveal that the H3-H3' dimer interface in the latter has become thermodynamically stable, in contrast to the former. Although the inter-sulphur distance of the two H3 cysteines in the oxidised native histone octamer has reduced to 6 A from the 7 A of the unoxidised form, analysis of the hydrogen bonds that constitute the (H4-H3)-(H3'-H4') tetramer indicates that the formation of a disulphide bond in the H3-H3' dimer interface is incompatible with stable tetramer formation. The biochemical and biophysical evidence, taken as a whole, is indicative of crystals that have a stable H3-H3' dimer interface, possibly extending to the interface within an isolated H3-H3' dimer, observed in SDS-PAGE gels.

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Organizational Affiliation: 

School of Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A-IV	A, E	129	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P02263 (Gallus gallus) Explore P02263  Go to UniProtKB:  P02263

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	B, F	126	Gallus gallus	Mutation(s): 0  Gene Names: H2B-I, H2B-II, H2B-III, H2B-IV, H2B-VI
UniProt
Find proteins for P0C1H3 (Gallus gallus) Explore P0C1H3  Go to UniProtKB:  P0C1H3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
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
UniProt
Find proteins for P84229 (Gallus gallus) Explore P84229  Go to UniProtKB:  P84229

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H4-VI	D, 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	I [auth A], O [auth B], R [auth C], Y [auth E], Z [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	AA [auth E], BA [auth F], CA [auth F], DA [auth F], EA [auth G], FA [auth G], GA [auth G], HA [auth G], IA [auth H], J [auth A], JA [auth H], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B], S [auth C], T [auth C], U [auth C], V [auth D], W [auth D], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.084	α = 90
b = 158.084	β = 90
c = 101.037	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-30 
Deposition Author(s): Wood, C.M., Sodngam, S., Nicholson, J.M., Lambert, S.J., Reynolds, C.D., Baldwin, J.P.

Revision History  

• Version 1.0: 2005-08-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance