3X1S

Crystal structure of the nucleosome core particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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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 transcription ...

    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: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1 AE135Homo sapiensMutation(s): 0 
Gene Names: 
h2aH3FAH3FBH3FCH3FDH3FFH3FHH3FIH3FJH3FK...

Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
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PHAROS:  P68431
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4 BF102Homo sapiensMutation(s): 0 
Gene Names: 
h2bH4/AH4/BH4/CH4/DH4/EH4/GH4/HH4/IH4/J...

Find proteins for P62805 (Homo sapiens)
Explore P62805 
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PHAROS:  P62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/E CG129Homo sapiensMutation(s): 0 
Gene Names: H2AFAH2AFMh3.1HIST1H2ABHIST1H2AEH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
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PHAROS:  P04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-B DH125Homo sapiensMutation(s): 0 
Gene Names: H2BFFH2BFQh4HIST1H2BBHIST2H2BEH2BC3
Find proteins for P33778 (Homo sapiens)
Explore P33778 
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PHAROS:  P33778
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (146-MER)I, J146synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.381α = 90
b = 109.363β = 90
c = 175.572γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release