1F66

2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.193 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a nucleosome core particle containing the variant histone H2A.Z.

Suto, R.K.Clarkson, M.J.Tremethick, D.J.Luger, K.

(2000) Nat Struct Biol 7: 1121-1124

  • DOI: 10.1038/81971
  • Primary Citation of Related Structures:  
    1F66

  • PubMed Abstract: 
  • Activation of transcription within chromatin has been correlated with the incorporation of the essential histone variant H2A.Z into nucleosomes. H2A.Z and other histone variants may establish structurally distinct chromosomal domains; however, the molecular mechanism by which they function is largely unknown ...

    Activation of transcription within chromatin has been correlated with the incorporation of the essential histone variant H2A.Z into nucleosomes. H2A.Z and other histone variants may establish structurally distinct chromosomal domains; however, the molecular mechanism by which they function is largely unknown. Here we report the 2.6 A crystal structure of a nucleosome core particle containing the histone variant H2A.Z. The overall structure is similar to that of the previously reported 2.8 A nucleosome structure containing major histone proteins. However, distinct localized changes result in the subtle destabilization of the interaction between the (H2A.Z-H2B) dimer and the (H3-H4)(2) tetramer. Moreover, H2A.Z nucleosomes have an altered surface that includes a metal ion. This altered surface may lead to changes in higher order structure, and/or could result in the association of specific nuclear proteins with H2A.Z. Finally, incorporation of H2A.Z and H2A within the same nucleosome is unlikely, due to significant changes in the interface between the two H2A.Z-H2B dimers.


    Organizational Affiliation

    Department of Biochemistry Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870 USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H3 AE136Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H4 BF103Mus musculusMutation(s): 0 
Gene Names: 
Find proteins for P62806 (Mus musculus)
Explore P62806 
Go to UniProtKB:  P62806
NIH Common Fund Data Resources
IMPC:  MGI:2448443
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H2A.Z CG128Homo sapiensMutation(s): 0 
Gene Names: H2AZ1H2AFZH2AZ
Find proteins for P0C0S5 (Homo sapiens)
Explore P0C0S5 
Go to UniProtKB:  P0C0S5
NIH Common Fund Data Resources
PHAROS:  P0C0S5
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H2B DH126Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
PALINDROMIC 146 BASE PAIR DNA FRAGMENTI, J146N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.66α = 90
b = 183.207β = 90
c = 109.922γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance