2ARO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1016/j.bbapap.2006.06.014

  • 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-H2 ...

    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.


    Organizational Affiliation

    School of Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK. c.m.wood@ljmu.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H2A-IV
A, E
129Gallus gallusMutation(s): 0 
Find proteins for P02263 (Gallus gallus)
Go to UniProtKB:  P02263
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
B, F
126Gallus gallusMutation(s): 0 
Gene Names: H2B-I, H2B-II, H2B-III, H2B-IV, H2B-VI
Find proteins for P0C1H3 (Gallus gallus)
Go to UniProtKB:  P0C1H3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3
C, G
136Gallus gallusMutation(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: 4
MoleculeChainsSequence LengthOrganismDetails
HISTONE H4-VI
D, H
103Gallus gallusMutation(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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 158.084α = 90.00
b = 158.084β = 90.00
c = 101.037γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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