1ZBB

Structure of the 4_601_167 Tetranucleosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.00 Å
  • R-Value Work: 0.386 
  • R-Value Observed: 0.386 

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This is version 1.3 of the entry. See complete history


Literature

X-ray structure of a tetranucleosome and its implications for the chromatin fibre.

Schalch, T.Duda, S.Sargent, D.F.Richmond, T.J.

(2005) Nature 436: 138-141

  • DOI: 10.1038/nature03686
  • Primary Citation of Related Structures:  
    1ZBB

  • PubMed Abstract: 
  • DNA in eukaryotic chromosomes is organized in arrays of nucleosomes compacted into chromatin fibres. This higher-order structure of nucleosomes is the substrate for DNA replication, recombination, transcription and repair. Although the structure of the nucleosome core is known at near-atomic resolution, even the most fundamental information about the organization of nucleosomes in the fibre is controversial ...

    DNA in eukaryotic chromosomes is organized in arrays of nucleosomes compacted into chromatin fibres. This higher-order structure of nucleosomes is the substrate for DNA replication, recombination, transcription and repair. Although the structure of the nucleosome core is known at near-atomic resolution, even the most fundamental information about the organization of nucleosomes in the fibre is controversial. Here we report the crystal structure of an oligonucleosome (a compact tetranucleosome) at 9 A resolution, solved by molecular replacement using the nucleosome core structure. The structure shows that linker DNA zigzags back and forth between two stacks of nucleosome cores, which form a truncated two-start helix, and does not follow a path compatible with a one-start solenoidal helix. The length of linker DNA is most probably buffered by stretching of the DNA contained in the nucleosome cores. We have built continuous fibre models by successively stacking tetranucleosomes one on another. The resulting models are nearly fully compacted and most closely resemble the previously described crossed-linker model. They suggest that the interfaces between nucleosomes along a single helix start are polymorphic.


    Organizational Affiliation

    ETH Zürich, Institute for Molecular Biology and Biophysics, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H3C [auth A],
G [auth E],
K [auth a],
O [auth e]
135Xenopus laevisMutation(s): 0 
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UniProt GroupP84233
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F],
L [auth b],
P [auth f]
102Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A.1E [auth C],
I [auth G],
M [auth c],
Q [auth g]
129Xenopus laevisMutation(s): 0 
UniProt
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UniProt GroupP06897
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B.1F [auth D],
J [auth H],
N [auth d],
R [auth h]
125Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA STRAND 1 (ARBITRARY MODEL SEQUENCE)A [auth I]347N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA STRAND 2 (ARBITRARY MODEL SEQUENCE)B [auth J]347N/A
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.00 Å
  • R-Value Work: 0.386 
  • R-Value Observed: 0.386 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.675α = 90
b = 168.445β = 90
c = 237.126γ = 90
Software Package:
Software NamePurpose
BEASTmodel building
REFMACrefinement
BEASTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-05-14
    Changes: Other