1U35

Crystal structure of the nucleosome core particle containing the histone domain of macroH2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of the histone variant macroH2A.

Chakravarthy, S.Gundimella, S.K.Caron, C.Perche, P.Y.Pehrson, J.R.Khochbin, S.Luger, K.

(2005) Mol.Cell.Biol. 25: 7616-7624

  • DOI: 10.1128/MCB.25.17.7616-7624.2005
  • Primary Citation of Related Structures:  1YD9

  • PubMed Abstract: 
  • macroH2A is an H2A variant with a highly unusual structural organization. It has a C-terminal domain connected to the N-terminal histone domain by a linker. Crystallographic and biochemical studies show that changes in the L1 loop in the histone fold ...

    macroH2A is an H2A variant with a highly unusual structural organization. It has a C-terminal domain connected to the N-terminal histone domain by a linker. Crystallographic and biochemical studies show that changes in the L1 loop in the histone fold region of macroH2A impact the structure and potentially the function of nucleosomes. The 1.6-A X-ray structure of the nonhistone region reveals an alpha/beta fold which has previously been found in a functionally diverse group of proteins. This region associates with histone deacetylases and affects the acetylation status of nucleosomes containing macroH2A. Thus, the unusual domain structure of macroH2A integrates independent functions that are instrumental in establishing a structurally and functionally unique chromatin domain.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E
136Mus musculusGene Names: Hist1h3a, Hist1h3g, Hist1h3h, Hist1h3i (H3a, H3.1-221, H3g, H3.1-291, H3h, H3.1-I, H3i)
Find proteins for P68433 (Mus musculus)
Go to UniProtKB:  P68433
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hist1h4i protein
B, F
103Mus musculusGene Names: Hist1h4a, Hist1h4b, Hist1h4c, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist4h4 (H4-53, H4-12, Hist2h4)
Find proteins for P62806 (Mus musculus)
Go to UniProtKB:  P62806
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
H2A histone family
C, G
120Homo sapiensGene Names: H2AFY (MACROH2A1)
Find proteins for O75367 (Homo sapiens)
Go to Gene View: H2AFY
Go to UniProtKB:  O75367
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
histone 3, H2ba
D, H
126Mus musculusGene Names: Hist3h2ba
Find proteins for Q9D2U9 (Mus musculus)
Go to UniProtKB:  Q9D2U9
Entity ID: 1
MoleculeChainsLengthOrganism
alpha-satellite DNAI,J146Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.505α = 90.00
b = 109.598β = 90.00
c = 175.989γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance