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- EMDB-24238: Melbournevirus nucleosome like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-24238
TitleMelbournevirus nucleosome like particle
Map dataMelbournevirus nucleosome like particle
Sample
  • Complex: Melbournevirus nucleosome like particle
    • Complex: Histone H4-H3 doublet, Histone H2B-H2A doublet
      • Protein or peptide: Histone H4-H3 doublet
      • Protein or peptide: Histone H2B-H2A doublet
    • Complex: DNA 147-mer
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)
Keywordsnucleosome / Virus / DNA BINDING PROTEIN / DNA BINDING 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 2A / Histone H2A / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone doublet H2B-H2A / Histone doublet H4-H3
Similarity search - Component
Biological speciesMelbournevirus / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsLiu Y / Toner CM
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2021
Title: Virus-encoded histone doublets are essential and form nucleosome-like structures.
Authors: Yang Liu / Hugo Bisio / Chelsea Marie Toner / Sandra Jeudy / Nadege Philippe / Keda Zhou / Samuel Bowerman / Alison White / Garrett Edwards / Chantal Abergel / Karolin Luger /
Abstract: The organization of genomic DNA into defined nucleosomes has long been viewed as a hallmark of eukaryotes. This paradigm has been challenged by the identification of "minimalist" histones in archaea ...The organization of genomic DNA into defined nucleosomes has long been viewed as a hallmark of eukaryotes. This paradigm has been challenged by the identification of "minimalist" histones in archaea and more recently by the discovery of genes that encode fused remote homologs of the four eukaryotic histones in Marseilleviridae, a subfamily of giant viruses that infect amoebae. We demonstrate that viral doublet histones are essential for viral infectivity, localize to cytoplasmic viral factories after virus infection, and ultimately are found in the mature virions. Cryogenic electron microscopy (cryo-EM) structures of viral nucleosome-like particles show strong similarities to eukaryotic nucleosomes despite the limited sequence identify. The unique connectors that link the histone chains contribute to the observed instability of viral nucleosomes, and some histone tails assume structural roles. Our results further expand the range of "organisms" that require nucleosomes and suggest a specialized function of histones in the biology of these unusual viruses.
History
DepositionJun 15, 2021-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.116
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.116
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7n8n
  • Surface level: 0.116
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24238.png

Downloads & links

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Map

FileDownload / File: emd_24238.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMelbournevirus nucleosome like particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 272.64 Å		1.07 Å/pix.
x 256 pix.
= 272.64 Å		1.07 Å/pix.
x 256 pix.
= 272.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.116 / Movie #1: 0.116
Minimum - Maximum-0.20754234 - 0.53330886
Average (Standard dev.)0.0019537504 (±0.017602345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z272.640272.640272.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2080.5330.002

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Supplemental data

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Mask #1

Fileemd_24238_msk_1.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 : Melbournevirus nucleosome like particle

EntireName: Melbournevirus nucleosome like particle
Components
  • Complex: Melbournevirus nucleosome like particle
    • Complex: Histone H4-H3 doublet, Histone H2B-H2A doublet
      • Protein or peptide: Histone H4-H3 doublet
      • Protein or peptide: Histone H2B-H2A doublet
    • Complex: DNA 147-mer
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)

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Supramolecule #1: Melbournevirus nucleosome like particle

SupramoleculeName: Melbournevirus nucleosome like particle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 218 KDa

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Supramolecule #2: Histone H4-H3 doublet, Histone H2B-H2A doublet

SupramoleculeName: Histone H4-H3 doublet, Histone H2B-H2A doublet / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Melbournevirus

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Supramolecule #3: DNA 147-mer

SupramoleculeName: DNA 147-mer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Histone H4-H3 doublet

MacromoleculeName: Histone H4-H3 doublet / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Melbournevirus
Molecular weightTheoretical: 26.73718 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKP IPNPLLGLDS TENLYFQGSS KAGKKVKAQQ HGHLADHVSV GETQIPKAST QHLLRKAGSL SAAGDTEVPI RGFVHMKLH KLVQKSLLAM QLAKRKTIMK SDVKKAAELM HLPVFAIPTK DSGAKGSVFL SCRQKGAGSA GTGSETNSQE V RSQMKSTC ...String:
MHHHHHHGKP IPNPLLGLDS TENLYFQGSS KAGKKVKAQQ HGHLADHVSV GETQIPKAST QHLLRKAGSL SAAGDTEVPI RGFVHMKLH KLVQKSLLAM QLAKRKTIMK SDVKKAAELM HLPVFAIPTK DSGAKGSVFL SCRQKGAGSA GTGSETNSQE V RSQMKSTC LIIPKERFRT MAKEISKKEG HDVHIAEAAL DMLQVIVESC TVRLLEKALV ITYSGKRTRV TSKDIETAFM LE HGPL

UniProtKB: Histone doublet H4-H3

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Macromolecule #2: Histone H2B-H2A doublet

MacromoleculeName: Histone H2B-H2A doublet / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Melbournevirus
Molecular weightTheoretical: 32.05816 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKP IPNPLLGLDS TENLYFQGSA TQKETTRKRD KSVNFRLGLR NMLAQIHPDI SVQTEALSEL SNIAVFLGKK ISHGAVTLL PEGTKTIKSS AVLLAAGDLY GKDLGRHAVG EMTKAVTRYG SAKESKEGSR SSKAKLQISV ARSERLLREH G GCSRVSEG ...String:
MHHHHHHGKP IPNPLLGLDS TENLYFQGSA TQKETTRKRD KSVNFRLGLR NMLAQIHPDI SVQTEALSEL SNIAVFLGKK ISHGAVTLL PEGTKTIKSS AVLLAAGDLY GKDLGRHAVG EMTKAVTRYG SAKESKEGSR SSKAKLQISV ARSERLLREH G GCSRVSEG AAVALAAAIE YFMGEVLELA GNAARDSKKV RISVKHITLA IQNDAALFAV VGKGVFSGAG VSLISVPIPR KK ARKTTEK EASSPKKKAA PKKKKAASKQ KKSLSDKELA KLTKKELAKY EKEQGMSPGY

UniProtKB: Histone doublet H2B-H2A

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Macromolecule #3: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
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: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
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

Concentration0.8 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34418
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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