3A6N

The nucleosome containing a testis-specific histone variant, human H3T

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T

Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H.

(2010) Proc Natl Acad Sci U S A 107: 10454-10459

  • DOI: 10.1073/pnas.1003064107
  • Primary Citation of Related Structures:  
    3A6N, 3AFA

  • PubMed Abstract: 

    • A histone H3 variant, H3T, is highly expressed in the testis, suggesting that it may play an important role in the chromatin reorganization required for meiosis and/or spermatogenesis. In the present study, we found that the nucleosome containing human H3T is significantly unstable both in vitro and in vivo, as compared to the conventional nucleosome containing H3 ...

    A histone H3 variant, H3T, is highly expressed in the testis, suggesting that it may play an important role in the chromatin reorganization required for meiosis and/or spermatogenesis. In the present study, we found that the nucleosome containing human H3T is significantly unstable both in vitro and in vivo, as compared to the conventional nucleosome containing H3.1. The crystal structure of the H3T nucleosome revealed structural differences in the H3T regions on both ends of the central alpha2 helix, as compared to those of H3.1. The H3T-specific residues (Met71 and Val111) are the source of the structural differences observed between H3T and H3.1. A mutational analysis revealed that these residues are responsible for the reduced stability of the H3T-containing nucleosome. These physical and structural properties of the H3T-containing nucleosome may provide the basis of chromatin reorganization during spermatogenesis.

    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1tA, E139Homo sapiensMutation(s): 0 
Gene Names: H3T, H3-4, H3FT, HIST3H3
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Find proteins for Q16695 (Homo sapiens)
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PHAROS:  Q16695
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UniProt GroupQ16695
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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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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC, G133Homo sapiensMutation(s): 0 
Gene Names: H2A, H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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UniProt GroupP04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H129Homo sapiensMutation(s): 0 
Gene Names: H2B, H2BC11, H2BFR, HIST1H2BJ
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Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
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Entity ID: 5
MoleculeChainsLengthOrganismImage
146-MER DNAI, J146N/A
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.476α = 90
b = 109.521β = 90
c = 181.052γ = 90
Software Package:
Software NamePurpose
BSSdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-07-18
    Changes: Structure summary