3WKJ

The nucleosome containing human TSH2B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of human nucleosome containing the testis-specific histone variant TSH2B.

Urahama, T.Horikoshi, N.Osakabe, A.Tachiwana, H.Kurumizaka, H.

(2014) Acta Crystallogr F Struct Biol Commun 70: 444-449

  • DOI: 10.1107/S2053230X14004695
  • Primary Citation of Related Structures:  
    3WKJ

  • PubMed Abstract: 
  • The human histone H2B variant TSH2B is highly expressed in testis and may function in the chromatin transition during spermatogenesis. In the present study, the crystal structure of the human testis-specific nucleosome containing TSH2B was determined at ...

    The human histone H2B variant TSH2B is highly expressed in testis and may function in the chromatin transition during spermatogenesis. In the present study, the crystal structure of the human testis-specific nucleosome containing TSH2B was determined at 2.8 Å resolution. A local structural difference between TSH2B and canonical H2B in nucleosomes was detected around the TSH2B-specific amino-acid residue Ser85. The TSH2B Ser85 residue does not interact with H4 in the nucleosome, but in the canonical nucleosome the H2B Asn84 residue (corresponding to the TSH2B Ser85 residue) forms water-mediated hydrogen bonds with the H4 Arg78 residue. In contrast, the other TSH2B-specific amino-acid residues did not induce any significant local structural changes in the TSH2B nucleosome. These findings may provide important information for understanding how testis-specific histone variants form nucleosomes during spermatogenesis.


    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1 AE139Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
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PHAROS:  P68431
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4 BF106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
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PHAROS:  P62805
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/E CG133Homo sapiensMutation(s): 0 
Gene Names: H2AH2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
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PHAROS:  P04908
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-A DH130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BATSH2BH2BC1
Find proteins for Q96A08 (Homo sapiens)
Explore Q96A08 
Go to UniProtKB:  Q96A08
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PHAROS:  Q96A08
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I, J146Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.037α = 90
b = 109.926β = 90
c = 182.961γ = 90
Software Package:
Software NamePurpose
BSSdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references