1HQ3

CRYSTAL STRUCTURE OF THE HISTONE-CORE-OCTAMER IN KCL/PHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the histone-core octamer in KCl/phosphate crystals at 2.15 A resolution.

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

(2003) Acta Crystallogr D Biol Crystallogr 59: 1395-1407

  • DOI: 10.1107/s0907444903011880
  • Primary Citation of Related Structures:  
    1HQ3

  • PubMed Abstract: 
  • The structure of the native chicken histone octamer, crystallized in 2 M KCl, 1.35 M potassium phosphate pH 6.9, has been refined at 2.15 A resolution to a final R factor of 21.4% and an R(free) of 25.2%. Unique crystal-packing interactions between h ...

    The structure of the native chicken histone octamer, crystallized in 2 M KCl, 1.35 M potassium phosphate pH 6.9, has been refined at 2.15 A resolution to a final R factor of 21.4% and an R(free) of 25.2%. Unique crystal-packing interactions between histone-core octamers are strong and one of them (area 4000 A(2)) involves two chloride ions and direct interactions between six acidic amino-acid residues on one octamer and the equivalent number of basic residues on the next. These interactions are on the structured part of the octamer (not involving tails). Five phosphate ions, 23 chloride ions and 437 water molecules have been identified in the structure. The phosphate and some chloride ions bind to basic amino-acid residues that interact with DNA in the nucleosome. The binding of most of the anions and the packing interactions are unique to these crystals. In other respects, and including the positions of four chloride ions, the octamer structure is very close to that of octamers in nucleosome-core particle crystals, particularly with respect to 'docking' sequences of the histone H2As and H4s. These sequences together with the H2B-H4 four-helix bundles stabilize the histone structure in the nucleosome and prevent the dissociation of the (H2A-H2B) dimers from the (H3-H4)(2) tetramer. Possible reasons why this happens at high salt in the absence of DNA are given.


    Organizational Affiliation

    Structural Biology, Galderma RandD, 635 Route des Lucioles, BP 87F-06902 Sophia Antipolis CEDEX, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H2A-IVAE129Gallus gallusMutation(s): 0 
Find proteins for P02263 (Gallus gallus)
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Go to UniProtKB:  P02263
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H2BBF126Gallus gallusMutation(s): 0 
Gene Names: H2B-VII
Find proteins for P0C1H5 (Gallus gallus)
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Go to UniProtKB:  P0C1H5
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H3CG136Gallus gallusMutation(s): 0 
Gene Names: H3-IH3-IIH3-IIIH3-IVH3-VH3-VIH3-VIIH3-VIII
Find proteins for P84229 (Gallus gallus)
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Go to UniProtKB:  P84229
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H4-VIDH103Gallus gallusMutation(s): 0 
Gene Names: H4-IH4-IIH4-IIIH4-IVH4-VH4-VIH4-VII
Find proteins for P62801 (Gallus gallus)
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Go to UniProtKB:  P62801
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

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: 2.15 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.56α = 90
b = 158.56β = 90
c = 102.48γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance