3X1U

Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

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Literature

Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming.

Padavattan, S.Shinagawa, T.Hasegawa, K.Kumasaka, T.Ishii, S.Kumarevel, T.

(2015) Biochem Biophys Res Commun 464: 929-935

  • DOI: 10.1016/j.bbrc.2015.07.070
  • Primary Citation of Related Structures:  
    3X1T, 3X1U, 3X1V, 3X1S

  • PubMed Abstract: 
  • Histone variants TH2a and TH2b are highly expressed in testes, oocytes and zygotes. Our recent analysis suggested that these histone variants enhance the induced generation of pluripotent stem cells (iPSCs) when co-expressed along with four transcrip ...

    Histone variants TH2a and TH2b are highly expressed in testes, oocytes and zygotes. Our recent analysis suggested that these histone variants enhance the induced generation of pluripotent stem cells (iPSCs) when co-expressed along with four transcription factors, Oct3/4, Sox2, Klf4 and c-Myc (OSKM), and are associated with an open chromatin structure [1]. In the present study, we report the crystal structures of nucleosomes (NCPs) with the mouse histone variants, TH2a and TH2b. The structures revealed two significant changes, as compared to the canonical counterparts: fewer histone-DNA contacts and changes in dimer-dimer interactions between TH2a-TH2a' (L1-loop). In vivo studies with domain swapping and point mutants of the variants revealed that the residues in the histone tails and the TH2a-L1 loop are important for reprogramming. Taken together, our work indicates that the NCP variants with structural modifications and flexible tails are most likely important for enhanced reprogramming of functions.


    Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Structural Biology Laboratory, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan. Electronic address: kumarevel.thirumananseri@riken.jp.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1AE135Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF102Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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PHAROS  P62805
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2ACG128Mus musculusMutation(s): 0 
Gene Names: H2AAH2ac1Hist1h2aa
Find proteins for Q8CGP4 (Mus musculus)
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Go to UniProtKB:  Q8CGP4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-BDH124Homo sapiensMutation(s): 0 
Gene Names: H2BH2BC3H2BFFHIST1H2BB
Find proteins for P33778 (Homo sapiens)
Explore P33778 
Go to UniProtKB:  P33778
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PHAROS  P33778
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (146-MER)I, J146synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.427α = 90
b = 109.184β = 90
c = 175.001γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description