7LV8

Structure of the Marseillevirus nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of a virus-encoded nucleosome.

Valencia-Sanchez, M.I.Abini-Agbomson, S.Wang, M.Lee, R.Vasilyev, N.Zhang, J.De Ioannes, P.La Scola, B.Talbert, P.Henikoff, S.Nudler, E.Erives, A.Armache, K.J.

(2021) Nat Struct Mol Biol 28: 413-417

  • DOI: 10.1038/s41594-021-00585-7
  • Primary Citation of Related Structures:  
    7LV9, 7LV8

  • PubMed Abstract: 
  • Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to the eukaryotic histone pairs H2B-H2A and H4-H3. These viral histones form 'forced' heterodimers, and a heterotetramer of four such heterodimers assembles DNA to form structures virtually identical to canonical eukaryotic nucleosomes ...

    Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to the eukaryotic histone pairs H2B-H2A and H4-H3. These viral histones form 'forced' heterodimers, and a heterotetramer of four such heterodimers assembles DNA to form structures virtually identical to canonical eukaryotic nucleosomes.


    Organizational Affiliation

    Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA. karim-jean.armache@nyulangone.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone doublet Delta-Gamma (Delta)A [auth B], E [auth F]97Marseillevirus marseillevirusMutation(s): 0 
Gene Names: MAR_ORF413
UniProt
Find proteins for D2XB48 (Marseillevirus marseillevirus)
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Go to UniProtKB:  D2XB48
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone doublet Delta-Gamma (Gamma)B [auth A], F [auth E]106Marseillevirus marseillevirusMutation(s): 0 
Gene Names: MAR_ORF413
UniProt
Find proteins for D2XB48 (Marseillevirus marseillevirus)
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Go to UniProtKB:  D2XB48
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone doublet Beta-Alpha (Beta)C [auth D], G [auth H]104Marseillevirus marseillevirusMutation(s): 0 
UniProt
Find proteins for A0A2R3ZQX0 (Marseillevirus Shanghai 1)
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Go to UniProtKB:  A0A2R3ZQX0
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone doublet Beta-Alpha (Alpha)D [auth C], H [auth G]165Marseillevirus marseillevirusMutation(s): 0 
Gene Names: MAR_ORF414
UniProt
Find proteins for D2XB49 (Marseillevirus marseillevirus)
Explore D2XB49 
Go to UniProtKB:  D2XB49
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (123-MER)I121synthetic construct
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (123-MER)J121synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
David and Lucile Packard FoundationUnited Statesna
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM115882-03

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references
  • Version 1.2: 2021-05-26
    Changes: Database references