3WA9

The nucleosome containing human H2A.Z.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2

Horikoshi, N.Sato, K.Shimada, K.Arimura, Y.Osakabe, A.Tachiwana, H.Hayashi-Takanaka, Y.Iwasaki, W.Kagawa, W.Harata, M.Kimura, H.Kurumizaka, H.

(2013) Acta Crystallogr.,Sect.D 69: 2431-2439

  • DOI: 10.1107/S090744491302252X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The histone H2A.Z variant is widely conserved among eukaryotes. Two isoforms, H2A.Z.1 and H2A.Z.2, have been identified in vertebrates and may have distinct functions in cell growth and gene expression. However, no structural differences between H2A. ...

    The histone H2A.Z variant is widely conserved among eukaryotes. Two isoforms, H2A.Z.1 and H2A.Z.2, have been identified in vertebrates and may have distinct functions in cell growth and gene expression. However, no structural differences between H2A.Z.1 and H2A.Z.2 have been reported. In the present study, the crystal structures of nucleosomes containing human H2A.Z.1 and H2A.Z.2 were determined. The structures of the L1 loop regions were found to clearly differ between H2A.Z.1 and H2A.Z.2, although their amino-acid sequences in this region are identical. This structural polymorphism may have been induced by a substitution that evolutionally occurred at the position of amino acid 38 and by the flexible nature of the L1 loops of H2A.Z.1 and H2A.Z.2. It was also found that in living cells nucleosomal H2A.Z.1 exchanges more rapidly than H2A.Z.2. A mutational analysis revealed that the amino-acid difference at position 38 is at least partially responsible for the distinctive dynamics of H2A.Z.1 and H2A.Z.2. These findings provide important new information for understanding the differences in the regulation and functions of H2A.Z.1 and H2A.Z.2 in cells.


    Organizational Affiliation

    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E
139Homo sapiensGene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Homo sapiensGene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A.Z
C, G
131Homo sapiensGene Names: H2AFZ (H2AZ)
Find proteins for P0C0S5 (Homo sapiens)
Go to Gene View: H2AFZ
Go to UniProtKB:  P0C0S5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
D, H
129Homo sapiensGene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens)
Go to Gene View: HIST1H2BJ
Go to UniProtKB:  P06899
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (146-MER)I,J146N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.903α = 90.00
b = 109.390β = 90.00
c = 181.764γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
BSSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release