5OXV

Structure of the 4_601_157 tetranucleosome (C2 form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.72 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.317 
  • R-Value Observed: 0.321 

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This is version 1.2 of the entry. See complete history


Literature

Capturing Structural Heterogeneity in Chromatin Fibers.

Ekundayo, B.Richmond, T.J.Schalch, T.

(2017) J Mol Biol 429: 3031-3042

  • DOI: 10.1016/j.jmb.2017.09.002
  • Primary Citation of Related Structures:  
    5OXV, 5OY7

  • PubMed Abstract: 
  • Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucleosomes with approximately 11-bp DNA linker length at 5 ...

    Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucleosomes with approximately 11-bp DNA linker length at 5.8 and 6.7 Å resolution. Minimal intramolecular nucleosome-nucleosome interactions result in a fiber model resembling a flat ribbon that is compatible with a two-start helical architecture, and that exposes histone and DNA surfaces to the environment. The differences in the two structures combined with electron microscopy reveal heterogeneous structural states, and we used site-specific chemical crosslinking to assess the diversity of nucleosome-nucleosome interactions through identification of structure-sensitive crosslink sites that provide a means to characterize fibers in solution. The chromatin fiber architectures observed here provide a basis for understanding heterogeneous chromatin higher-order structures as they occur in a genomic context.


    Organizational Affiliation

    Department of Molecular Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211 Geneva 4, Switzerland. Electronic address: thomas.schalch@unige.ch.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1O [auth D], K [auth H], F [auth N], B [auth R]126Xenopus laevisMutation(s): 0 
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Find proteins for P02281 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AP [auth C], L [auth G], G [auth M], C [auth Q]130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4Q [auth B], M [auth F], H [auth L], D [auth P]102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2R [auth A], N [auth E], I [auth K], E [auth O]135Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA STRAND 1 (601-based sequence model)A [auth J]312synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA STRAND 2 (601-based sequence model)J [auth I]313synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.72 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.317 
  • R-Value Observed: 0.321 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 348.839α = 90
b = 63.274β = 124.74
c = 271.361γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandPP00P3-139137
Swiss National Science FoundationSwitzerlandPP00P3_163760
Swiss National Science FoundationSwitzerlandPP00P3_172904

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations