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- EMDB-45966: Melbournevirus Mini variant Nucleosome -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-45966
TitleMelbournevirus Mini variant Nucleosome
Map data
Sample
  • Complex: Melbourne nucleosome mini variant
    • Complex: Melbourne nucleosome mini variant histone doublet proteins
      • Protein or peptide: Histone doublet miniH2B-H2A
      • Protein or peptide: Histone doublet H4-H3
    • Complex: Widom 601 DNA
      • DNA: Widom 601 Strand 1
      • DNA: Widom 601 Strand 2
KeywordsHistone / 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 / Histone-fold
Similarity search - Domain/homology
Histone doublet miniH2B-H2A / Histone doublet H4-H3
Similarity search - Component
Biological speciesMelbournevirus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.41 Å
AuthorsVillalta A / Luger K
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45966.png

Downloads & links

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Map

FileDownload / File: emd_45966.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.49 Å/pix.
x 448 pix.
= 217.28 Å		0.49 Å/pix.
x 448 pix.
= 217.28 Å		0.49 Å/pix.
x 448 pix.
= 217.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.485 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0222
Minimum - Maximum-0.050159745 - 0.09790043
Average (Standard dev.)0.0007370428 (±0.004613047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 217.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45966_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45966_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Melbourne nucleosome mini variant

EntireName: Melbourne nucleosome mini variant
Components
  • Complex: Melbourne nucleosome mini variant
    • Complex: Melbourne nucleosome mini variant histone doublet proteins
      • Protein or peptide: Histone doublet miniH2B-H2A
      • Protein or peptide: Histone doublet H4-H3
    • Complex: Widom 601 DNA
      • DNA: Widom 601 Strand 1
      • DNA: Widom 601 Strand 2

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Supramolecule #1: Melbourne nucleosome mini variant

SupramoleculeName: Melbourne nucleosome mini variant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Melbourne nucleosome mini variant histone doublet proteins

SupramoleculeName: Melbourne nucleosome mini variant histone doublet proteins
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Melbournevirus

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Supramolecule #3: Widom 601 DNA

SupramoleculeName: Widom 601 DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Histone doublet miniH2B-H2A

MacromoleculeName: Histone doublet miniH2B-H2A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Melbournevirus
Molecular weightTheoretical: 19.168326 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDRVGKYGLF IKRISPKDAD ITKESLETVN NMLVFLAEKL TKQANIIIDQ KTLRHDAFLW LLTDIQGELG KHSQDFANSV LYGEKELVF PTKRTENLMR KNTCLRISQS AVKTLTAILE YFCGQIMEAS FSQAKKSKRK RIRPIDIEAA ISQDKELHSM F GKGVISGR

UniProtKB: Histone doublet miniH2B-H2A

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Macromolecule #2: Histone doublet H4-H3

MacromoleculeName: Histone doublet H4-H3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Melbournevirus
Molecular weightTheoretical: 23.56468 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKAGKKVKA QQHGHLADHV SVGETQIPKA STQHLLRKAG SLSAAGDTEV PIRGFVHMKL HKLVQKSLLA MQLAKRKTIM KSDVKKAAE LMHLPVFAIP TKDSGAKGSV FLSCRQKGAG SAGTGSETNS QEVRSQMKST CLIIPKERFR TMAKEISKKE G HDVHIAEA ...String:
MSKAGKKVKA QQHGHLADHV SVGETQIPKA STQHLLRKAG SLSAAGDTEV PIRGFVHMKL HKLVQKSLLA MQLAKRKTIM KSDVKKAAE LMHLPVFAIP TKDSGAKGSV FLSCRQKGAG SAGTGSETNS QEVRSQMKST CLIIPKERFR TMAKEISKKE G HDVHIAEA ALDMLQVIVE SCTVRLLEKA LVITYSGKRT RVTSKDIETA FMLEHGPL

UniProtKB: Histone doublet H4-H3

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Macromolecule #3: Widom 601 Strand 1

MacromoleculeName: Widom 601 Strand 1 / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.153781 KDa
SequenceString: (DA)(DT)(DC)(DT)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DA)(DT)(DC)(DT)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DG)(DA)(DT)

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Macromolecule #4: Widom 601 Strand 2

MacromoleculeName: Widom 601 Strand 2 / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.594043 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC) (DA)(DG)(DA)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36051
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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