1TZY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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 61: 541-545

  • DOI: 10.1107/S1744309105013813

  • 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 o ...

    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.


    Organizational Affiliation

    School of Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, England. c.m.wood@livjm.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H2A-IV
A, E
129Gallus gallusN/A
Find proteins for P02263 (Gallus gallus)
Go to UniProtKB:  P02263
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
B, F
126Gallus gallusGene Names: H2B-VII
Find proteins for P0C1H5 (Gallus gallus)
Go to UniProtKB:  P0C1H5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3
C, G
136Gallus gallusGene 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 gallusGene 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: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 158.351α = 90.00
b = 158.351β = 90.00
c = 103.576γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PXGENdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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