1TZY

Crystal Structure of the Core-Histone Octamer to 1.90 Angstrom Resolution

• PDB DOI:  https://doi.org/10.2210/pdb1TZY/pdb

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


• Deposited: 2004-07-12 Released: 2004-08-03 
• Deposition Author(s): Wood, C.M., Nicholson, J.M., Chantalat, L., Reynolds, C.D., Lambert, S.J., Baldwin, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

High-resolution structure of the native histone octamer.

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

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 541-545

• PubMed: 16511091 
• DOI: https://doi.org/10.1107/S1744309105013813
• Primary Citation of Related Structures:  
  1TZY


• PubMed Abstract: 
  

Crystals of native histone octamers (H2A-H2B)-(H4-H3)-(H3'-H4')-(H2B'-H2A') from chick erythrocytes in 2 M KCl, 1.35 M potassium phosphate pH 6.9 diffract X-rays to 1.90 A resolution, yielding a structure with an R(work) value of 18.7% and an Rfree of 22.2%. The crystal space group is P6(5), the asymmetric unit of which contains one complete octamer. This high-resolution model of the histone-core octamer allows further insight into intermolecular interactions, including water molecules, that dock the histone dimers to the tetramer in the nucleosome-core particle and have relevance to nucleosome remodelling. The three key areas analysed are the H2A'-H3-H4 molecular cluster (also H2A-H3'-H4'), the H4-H2B' interaction (also H4'-H2B) and the H2A'-H4 beta-sheet interaction (also H2A-H4'). The latter of these three regions is important to nucleosome remodelling by RNA polymerase II, as it is shown to be a likely core-histone binding site, and its disruption creates an instability in the nucleosome-core particle. A majority of the water molecules in the high-resolution octamer have positions that correlate to similar positions in the high-resolution nucleosome-core particle structure, suggesting that the high-resolution octamer model can be used for comparative studies with the high-resolution nucleosome-core particle.

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Organizational Affiliation: 

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

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: 6,625 
• Modelled Residue Count: 755 
• Deposited Residue Count: 988 
• Unique protein chains: 4

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-VII
UniProt
Find proteins for P0C1H5 (Gallus gallus) Explore P0C1H5  Go to UniProtKB:  P0C1H5

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], N [auth B], Q [auth C], X [auth E], Y [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	AA [auth E], BA [auth F], CA [auth F], DA [auth G], EA [auth G], FA [auth G], GA [auth G], HA [auth H], IA [auth H], J [auth A], JA [auth H], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], U [auth D], V [auth D], W [auth D], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.351	α = 90
b = 158.351	β = 90
c = 103.576	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PXGEN	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-03 
Deposition Author(s): Wood, C.M., Nicholson, J.M., Chantalat, L., Reynolds, C.D., Lambert, S.J., Baldwin, J.P.

Revision History  

• Version 1.0: 2004-08-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance