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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: To Be Published
Title: Melbournevirus Mini variant Nucleosome
Authors: Villalta A / Luger K
History
DepositionJul 29, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 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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