6JOU

Crystal structure of the human nucleosome containing H2A.Z.1 S42R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Literature

Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo.

Horikoshi, N.Kujirai, T.Sato, K.Kimura, H.Kurumizaka, H.

(2019) Biochem Biophys Res Commun 515: 719-724

  • DOI: 10.1016/j.bbrc.2019.06.012
  • Primary Citation of Related Structures:  
    6JOU

  • PubMed Abstract: 
  • The nucleosome containing the histone H2A.Z.1 variant is unstable, as compared to the canonical nucleosome in vitro, and the incorporation of H2A.Z.1 into chromatin is less stable than that of the canonical H2A in vivo. In the present study, we designed a human H2A ...

    The nucleosome containing the histone H2A.Z.1 variant is unstable, as compared to the canonical nucleosome in vitro, and the incorporation of H2A.Z.1 into chromatin is less stable than that of the canonical H2A in vivo. In the present study, we designed a human H2A.Z.1(S42R) mutant, in which the Ser42 residue is replaced by Arg. In the crystal structure of the nucleosome containing H2A.Z.1(S42R), the Arg residue inserted at the H2A.Z.1-Ser42 position forms additional hydrogen bonds and electrostatic interactions with the DNA backbone phosphates. The Arg42 residue is located in the L1-loop region of H2A.Z.1, but the backbone geometry of the L1-loop is not affected by the H2A.Z.1(S42R) substitution. The nucleosome containing H2A.Z.1(S42R) exhibited enhanced thermal stability, as compared to that containing wild-type H2A.Z.1 in vitro. Fluorescence recovery after photobleaching experiments revealed that H2A.Z.1(S42R) was more stably incorporated in chromatin than wild-type H2A.Z.1 in living cells. Therefore, the H2A.Z.1(S42R) mutant stabilizes the nucleosome in vitro and in vivo, and may be useful as a tool to study the functional significance of the unstable nature of the H2A.Z.1 nucleosome.


    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; Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan. Electronic address: kurumizaka@iam.u-tokyo.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1A, E139Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F106Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A.ZC, G131Homo sapiensMutation(s): 1 
Gene Names: H2AFZH2AZH2AZ1
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Find proteins for P0C0S5 (Homo sapiens)
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PHAROS:  P0C0S5
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
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Find proteins for P06899 (Homo sapiens)
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (146-MER)I, J146Homo sapiens
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.955α = 90
b = 108.17β = 90
c = 169.812γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
BSSdata collection

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP25116002

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references, Derived calculations