3WTP

Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3

Arimura, Y.Shirayama, K.Horikoshi, N.Fujita, R.Taguchi, H.Kagawa, W.Fukagawa, T.Almouzni, G.Kurumizaka, H.

(2014) Sci Rep 4: 7115-7115

  • DOI: 10.1038/srep07115
  • Primary Citation of Related Structures:  
    3WTP

  • PubMed Abstract: 
  • The centromere-specific histone H3 variant, CENP-A, is overexpressed in particular aggressive cancer cells, where it can be mislocalized ectopically in the form of heterotypic nucleosomes containing H3.3. In the present study, we report the crystal s ...

    The centromere-specific histone H3 variant, CENP-A, is overexpressed in particular aggressive cancer cells, where it can be mislocalized ectopically in the form of heterotypic nucleosomes containing H3.3. In the present study, we report the crystal structure of the heterotypic CENP-A/H3.3 particle and reveal its "hybrid structure", in which the physical characteristics of CENP-A and H3.3 are conserved independently within the same particle. The CENP-A/H3.3 nucleosome forms an unexpectedly stable structure as compared to the CENP-A nucleosome, and allows the binding of the essential centromeric protein, CENP-C, which is ectopically mislocalized in the chromosomes of CENP-A overexpressing cells.


    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-like centromeric protein AA143Homo sapiensMutation(s): 0 
Gene Names: CENPA
Find proteins for P49450 (Homo sapiens)
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Go to UniProtKB:  P49450
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PHAROS  P49450
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF106Homo sapiensMutation(s): 0 
Gene Names: 
H3.3H4/AH4/BH4/CH4/DH4/EH4/GH4/HH4/IH4/J...

Find proteins for P62805 (Homo sapiens)
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PHAROS  P62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/ECG133Homo sapiensMutation(s): 0 
Gene Names: H2AFAH2AFMH4HIST1H2ABHIST1H2AEH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
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PHAROS  P04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JDH129Homo sapiensMutation(s): 0 
Gene Names: H2AH2BFRHIST1H2BJH2BC11
Find proteins for P06899 (Homo sapiens)
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PHAROS  P06899
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3E140Homo sapiensMutation(s): 0 
Gene Names: H2BH3.3AH3.3BH3F3H3F3AH3F3BPP781H3-3AH3-3B
Find proteins for P84243 (Homo sapiens)
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PHAROS  P84243
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (146-MER)I, J146Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.117α = 90
b = 107.667β = 90
c = 168.143γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description