3AV2

The human nucleosome structure containing the histone variant H3.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of human nucleosomes containing major histone H3 variants

Tachiwana, H.Osakabe, A.Shiga, T.Miya, Y.Kimura, H.Kagawa, W.Kurumizaka, H.

(2011) Acta Crystallogr D Biol Crystallogr 67: 578-583

  • DOI: 10.1107/S0907444911014818
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The nucleosome is the fundamental repeating unit of chromatin, via which genomic DNA is packaged into the nucleus in eukaryotes. In the nucleosome, two copies of each core histone, H2A, H2B, H3 and H4, form a histone octamer which wraps 146 base pair ...

    The nucleosome is the fundamental repeating unit of chromatin, via which genomic DNA is packaged into the nucleus in eukaryotes. In the nucleosome, two copies of each core histone, H2A, H2B, H3 and H4, form a histone octamer which wraps 146 base pairs of DNA around itself. All of the core histones except for histone H4 have nonallelic isoforms called histone variants. In humans, eight histone H3 variants, H3.1, H3.2, H3.3, H3T, H3.5, H3.X, H3.Y and CENP-A, have been reported to date. Previous studies have suggested that histone H3 variants possess distinct functions in the formation of specific chromosome regions and/or in the regulation of transcription and replication. H3.1, H3.2 and H3.3 are the most abundant H3 variants. Here, crystal structures of human nucleosomes containing either H3.2 or H3.3 have been solved. The structures were essentially the same as that of the H3.1 nucleosome. Since the amino-acid residues specific for H3.2 and H3.3 are located on the accessible surface of the H3/H4 tetramer, they may be potential interaction sites for H3.2- and H3.3-specific chaperones.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3A, E139Homo sapiensMutation(s): 0 
Gene Names: H3.3H3-3AH3.3AH3F3H3F3APP781H3-3BH3.3BH3F3B
Find proteins for P84243 (Homo sapiens)
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Go to UniProtKB:  P84243
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PHAROS  P84243
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4B, F106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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PHAROS  P62805
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/EC, G133Homo 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 LengthOrganismDetails
Histone H2B type 1-JD, H129Homo sapiensMutation(s): 0 
Gene Names: H2BH2BC11H2BFRHIST1H2BJ
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
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PHAROS  P06899
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganism
146-MER DNAI, J146N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.843α = 90
b = 109.686β = 90
c = 181.177γ = 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 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2012-07-18
    Changes: Structure summary