9CVT | pdb_00009cvt

Melbournevirus Mini variant Nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Melbournevirus encodes a shorter H2B-H2A doublet histone variant that forms structurally distinct nucleosome structures.

Villalta, A.Bisio, H.Toner, C.M.Abergel, C.Luger, K.

(2025) Nat Commun 16: 6903-6903

  • DOI: https://doi.org/10.1038/s41467-025-62031-2
  • Primary Citation of Related Structures:  
    9CVT

  • PubMed Abstract: 

    Unique among viruses, some giant viruses utilize histones to organize their genomes into nucleosomes. Melbournevirus encodes a distinct H2B-H2A histone doublet variant in addition to the canonical H4-H3 and H2B-H2A doublets. This viral histone variant has a truncated H2B portion and its amino acid sequence deviates from that of the main viral H2B-H2A throughout the entire coding region. It is less abundant than the main H2B-H2A doublet, is likely essential for melbournevirus fitness, and is conserved in all Marseilleviridae. The cryo-EM structure of a nucleosome-like particle reconstituted with this H2B-H2A variant and viral H4-H3 reveals that only 90 base pairs of DNA are stably bound, significantly less than in eukaryotic nucleosomes and viral nucleosomes made with the main fused viral histone doublets. The reduced ability to bind DNA can be attributed to structural differences between variant and main H2B-H2A. Variant melbournevirus nucleosomes are less stable, possibly aiding rapid genome unpacking to initiate gene expression. Our results highlight the remarkable propensity of giant viruses to appropriate the utility of histones for their specialized purposes.


  • Organizational Affiliation
    • Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone doublet miniH2B-H2A
A, B
168Marseillevirus sp. 'MelbournevirusMutation(s): 0 
Gene Names: MEL_149
UniProt
Find proteins for A0A097I1R9 (Melbournevirus)
Explore A0A097I1R9 
Go to UniProtKB:  A0A097I1R9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097I1R9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone doublet H4-H3
C, D
216Marseillevirus sp. 'MelbournevirusMutation(s): 0 
Gene Names: MEL_368
UniProt
Find proteins for A0A097I2D0 (Melbournevirus)
Explore A0A097I2D0 
Go to UniProtKB:  A0A097I2D0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097I2D0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
Widom 601 Strand 1E [auth I]147synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
Widom 601 Strand 2F [auth J]147synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references