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- PDB-9cvt: Melbournevirus Mini variant Nucleosome -

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Basic information

Entry
Database: PDB / ID: 9cvt
TitleMelbournevirus Mini variant Nucleosome
Components
  • Histone doublet H4-H3
  • Histone doublet miniH2B-H2A
  • Widom 601 Strand 1
  • Widom 601 Strand 2
KeywordsVIRAL PROTEIN/DNA / Histone / Nucleosome / Virus / VIRAL PROTEIN / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


chromosome condensation / virion component / structural constituent of chromatin / host cell cytoplasm / protein heterodimerization activity / host cell nucleus / DNA binding
Similarity search - Function
Histone H2A / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone doublet miniH2B-H2A / Histone doublet H4-H3
Similarity search - Component
Biological speciesMelbournevirus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.41 Å
AuthorsVillalta, A. / Luger, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2025
Title: Melbournevirus encodes a shorter H2B-H2A doublet histone variant that forms structurally distinct nucleosome structures.
Authors: Alejandro Villalta / Hugo Bisio / Chelsea M Toner / Chantal Abergel / Karolin Luger /
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- ...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.
History
DepositionJul 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone doublet miniH2B-H2A
B: Histone doublet miniH2B-H2A
C: Histone doublet H4-H3
D: Histone doublet H4-H3
I: Widom 601 Strand 1
J: Widom 601 Strand 2


Theoretical massNumber of molelcules
Total (without water)176,2146
Polymers176,2146
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Histone doublet miniH2B-H2A / Histone miniH2B-H2A fusion protein / MV-miniH2B-H2A


Mass: 19168.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melbournevirus / Gene: MEL_149 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A097I1R9
#2: Protein Histone doublet H4-H3 / Histone H4-H3 fusion protein / MV-H4-H3


Mass: 23564.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melbournevirus / Gene: MEL_368 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A097I2D0
#3: DNA chain Widom 601 Strand 1


Mass: 45153.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: DNA chain Widom 601 Strand 2


Mass: 45594.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Melbourne nucleosome mini variantCOMPLEXall0MULTIPLE SOURCES
2Melbourne nucleosome mini variant histone doublet proteinsCOMPLEX#1-#21RECOMBINANT
3Widom 601 DNACOMPLEX#3-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Melbournevirus1560514
33synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 20000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36051 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049417
ELECTRON MICROSCOPYf_angle_d0.70613464
ELECTRON MICROSCOPYf_dihedral_angle_d32.9622504
ELECTRON MICROSCOPYf_chiral_restr0.0381561
ELECTRON MICROSCOPYf_plane_restr0.0041049

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