7LV9

Marseillevirus heterotrimeric (hexameric) nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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: https://doi.org/10.1038/s41594-021-00585-7
  • Primary Citation of Related Structures:  
    7LV8, 7LV9

  • 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.


  • Organizational Affiliation

    Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence 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)
Explore D2XB48 
Go to UniProtKB:  D2XB48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2XB48
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence 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)
Explore D2XB48 
Go to UniProtKB:  D2XB48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2XB48
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone doublet Beta-Alpha (Beta)C [auth D]104Marseillevirus marseillevirusMutation(s): 0 
UniProt
Find proteins for D2XB49 (Marseillevirus marseillevirus)
Explore D2XB49 
Go to UniProtKB:  D2XB49
Entity Groups  
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UniProt GroupD2XB49
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone doublet Beta-Alpha (Alpha)D [auth C]165Marseillevirus marseillevirusMutation(s): 0 
Gene Names: MAR_ORF414
UniProt
Find proteins for D2XB49 (Marseillevirus marseillevirus)
Explore D2XB49 
Go to UniProtKB:  D2XB49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2XB49
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (96-MER)95synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (96-MER)95synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



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