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- EMDB-42053: Medusavirus Nucleosome Core Particle -

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Basic information

Entry
Database: EMDB / ID: EMD-42053
TitleMedusavirus Nucleosome Core Particle
Map data
Sample
  • Complex: Medusavirus Nucleosome Core Particle
    • Complex: Histone Complex
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: WIDOM 601 DNA
      • DNA: WIDOM 601 DNA strand 1
      • DNA: WIDOM 601 DNA strand 2
KeywordsDNA Protein Complex / Nucleosome / Giant Virus / NCLDV / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Biological speciesMedusavirus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsToner CM / Hoitsma NM / Weerawarana S / Luger K
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2024
Title: Characterization of Medusavirus encoded histones reveals nucleosome-like structures and a unique linker histone.
Authors: Chelsea M Toner / Nicole M Hoitsma / Sashi Weerawarana / Karolin Luger /
Abstract: The organization of DNA into nucleosomes is a ubiquitous and ancestral feature that was once thought to be exclusive to the eukaryotic domain of life. Intriguingly, several representatives of the ...The organization of DNA into nucleosomes is a ubiquitous and ancestral feature that was once thought to be exclusive to the eukaryotic domain of life. Intriguingly, several representatives of the Nucleocytoplasmic Large DNA Viruses (NCLDV) encode histone-like proteins that in Melbournevirus were shown to form nucleosome-like particles. Medusavirus medusae (MM), a distantly related giant virus, encodes all four core histone proteins and, unique amongst most giant viruses, a putative acidic protein with two domains resembling eukaryotic linker histone H1. Here, we report the structure of nucleosomes assembled with MM histones and highlight similarities and differences with eukaryotic and Melbournevirus nucleosomes. Our structure provides insight into how variations in histone tail and loop lengths are accommodated within the context of the nucleosome. We show that MM-histones assemble into tri-nucleosome arrays, and that the putative linker histone H1 does not function in chromatin compaction. These findings expand our limited understanding of chromatin organization by virus-encoded histones.
History
DepositionSep 20, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42053.png

Downloads & links

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Map

FileDownload / File: emd_42053.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 336 pix.
= 325.92 Å		0.97 Å/pix.
x 336 pix.
= 325.92 Å		0.97 Å/pix.
x 336 pix.
= 325.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.38585216 - 0.73105
Average (Standard dev.)0.000245733 (±0.015536748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 325.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_42053_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_42053_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 : Medusavirus Nucleosome Core Particle

EntireName: Medusavirus Nucleosome Core Particle
Components
  • Complex: Medusavirus Nucleosome Core Particle
    • Complex: Histone Complex
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: WIDOM 601 DNA
      • DNA: WIDOM 601 DNA strand 1
      • DNA: WIDOM 601 DNA strand 2

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Supramolecule #1: Medusavirus Nucleosome Core Particle

SupramoleculeName: Medusavirus Nucleosome Core Particle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Histone Complex

SupramoleculeName: Histone Complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Medusavirus

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Supramolecule #3: WIDOM 601 DNA

SupramoleculeName: WIDOM 601 DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Medusavirus
Molecular weightTheoretical: 21.766553 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMPKERAI KKSKSAVKKV AEKKAAIKSK AKKAATGVKK PHRFRPGTTA KRLSKKEQK LSSTKTTVRR APFGRIVRTI ASLSSADSMR FSANAVDLLQ QGIELYMLDL MKNAALAAKQ AKRMTLMGKD I DLIQTANH ...String:
MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMPKERAI KKSKSAVKKV AEKKAAIKSK AKKAATGVKK PHRFRPGTTA KRLSKKEQK LSSTKTTVRR APFGRIVRTI ASLSSADSMR FSANAVDLLQ QGIELYMLDL MKNAALAAKQ AKRMTLMGKD I DLIQTANH EMIDEAHAAK LANTSSAGFA RRRVTKKE

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Medusavirus
Molecular weightTheoretical: 14.043632 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMPKKIAA RRSSKHIKNL GEEIGNSAVR KTVLRTGVVF RLDKTVRPKF HKVMLSKLY EAVNIAKLAA KHSGRSTIQP KDVRLGLKLA SIKLLA

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Medusavirus
Molecular weightTheoretical: 28.382625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMEIDSHV QPAEVLAAAS ESMQLEEQTQ LPASAAGEAL EELQTEGKKT SPAKKRTSS GKNVKRANER AGLKLPPGRI QKIIKANQTT DVGRSSPTAS VFLTAVIEDI VKEIIKGADK KSEERGRIRI S PQDILKYL ...String:
MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMEIDSHV QPAEVLAAAS ESMQLEEQTQ LPASAAGEAL EELQTEGKKT SPAKKRTSS GKNVKRANER AGLKLPPGRI QKIIKANQTT DVGRSSPTAS VFLTAVIEDI VKEIIKGADK KSEERGRIRI S PQDILKYL TENGEAYMHI LGDAFVSHGG VGQVAEMAAA AANTGIKKRK RAASTAEGAP KKKIAKKAAA KKATGAKKVV KK KSGSTKS KTTGKSVTKK ASSRKVASA

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Medusavirus
Molecular weightTheoretical: 24.104611 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMSQIDEH VTEMTEFEAE HESTYSEHSD EEEQELGARV PSRKQKGKAA AKKVKKAVA KKSGEERRRK KNYDSFATFI AKLVGPNGKG RKPGFSAKGM EVLESIVKSL ATEMTIVANE LAKHQGRQTL G AGDFRTAL ...String:
MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMSQIDEH VTEMTEFEAE HESTYSEHSD EEEQELGARV PSRKQKGKAA AKKVKKAVA KKSGEERRRK KNYDSFATFI AKLVGPNGKG RKPGFSAKGM EVLESIVKSL ATEMTIVANE LAKHQGRQTL G AGDFRTAL AVRGSLIARE PATVKALTEM GEKAVLKYQS SLGRPAKTAP KKKKATKKAS A

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Macromolecule #5: WIDOM 601 DNA strand 1

MacromoleculeName: WIDOM 601 DNA strand 1 / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 63.576527 KDa
SequenceString: (DA)(DT)(DC)(DT)(DA)(DG)(DT)(DA)(DT)(DT) (DA)(DA)(DT)(DT)(DA)(DA)(DT)(DA)(DT)(DG) (DA)(DA)(DT)(DT)(DC)(DG)(DG)(DA)(DT) (DC)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC) (DA) (DG)(DG)(DA)(DT)(DG)(DT) ...String:
(DA)(DT)(DC)(DT)(DA)(DG)(DT)(DA)(DT)(DT) (DA)(DA)(DT)(DT)(DA)(DA)(DT)(DA)(DT)(DG) (DA)(DA)(DT)(DT)(DC)(DG)(DG)(DA)(DT) (DC)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC) (DA) (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)(DA)(DT) (DC) (DG)(DG)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC) (DG)(DT)(DA)(DT)(DA)(DG)(DG)(DG)(DT) (DC)(DC)(DG)(DA)(DT)

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Macromolecule #6: WIDOM 601 DNA strand 2

MacromoleculeName: WIDOM 601 DNA strand 2 / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 63.007145 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC) (DG)(DC)(DC)(DC)(DG)(DA)(DT)(DG)(DA) (DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG) (DA)(DG)(DG)(DC)(DC)(DG) ...String:
(DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC) (DG)(DC)(DC)(DC)(DG)(DA)(DT)(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)(DT)(DG)(DT)(DG)(DC)(DA)(DT) (DG)(DT)(DG)(DG)(DA)(DT)(DC)(DC) (DG) (DA)(DA)(DT)(DT)(DC)(DA)(DT)(DA)(DT)(DT) (DA)(DA)(DT)(DT)(DA)(DA)(DT)(DA)(DC) (DT)(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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClSodium Chloride
20.0 mMTris-Hydrochloric acid
5.0 mMDithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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: 1.7 µm / Nominal defocus min: 0.6 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159734
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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