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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE H3C [auth A],
G [auth E]
136Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE H4D [auth B],
H [auth F]
103Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62806 (Mus musculus)
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IMPC:  MGI:2448443
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UniProt GroupP62806
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE H2A.ZE [auth C],
I [auth G]
128Homo sapiensMutation(s): 0 
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Find proteins for P0C0S5 (Homo sapiens)
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Go to UniProtKB:  P0C0S5
PHAROS:  P0C0S5
GTEx:  ENSG00000164032 
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UniProt GroupP0C0S5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE H2BF [auth D],
J [auth H]
126Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
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UniProt GroupP02281
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Entity ID: 1
MoleculeChains LengthOrganismImage
PALINDROMIC 146 BASE PAIR DNA FRAGMENTA [auth I],
B [auth J]
146N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
K [auth I]
L [auth I]
M [auth I]
N [auth I]
O [auth I]
K [auth I],
L [auth I],
M [auth I],
N [auth I],
O [auth I],
P [auth I],
Q [auth I],
R [auth J],
S [auth J],
T [auth J],
U [auth J],
V [auth J],
W [auth C],
X [auth E],
Y [auth G]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
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
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations