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- EMDB-23529: Structure of the Marseillevirus nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-23529
TitleStructure of the Marseillevirus nucleosome
Map dataStructure of Marseillevirus nucleosome, main map
Sample
  • Complex: Structure of the Marseillevirus nucleosome
    • Protein or peptide: Histone doublet Delta-Gamma (Delta)
    • Protein or peptide: Histone doublet Delta-Gamma (Gamma)
    • Protein or peptide: Histone doublet Beta-Alpha (Beta)
    • Protein or peptide: Histone doublet Beta-Alpha (Alpha)
    • DNA: DNA (123-MER)
    • DNA: DNA (123-MER)
KeywordsStructural Protein/DNA / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding
Similarity search - Function
Histone H2A / Histone 2A / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B/H2A fusion protein / Histone H3 / Histone H2B/H2A fusion protein
Similarity search - Component
Biological speciessynthetic construct (others) / Marseillevirus marseillevirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsValencia-Sanchez MI / Abini-Agbomson S
Funding support United States, 2 items
OrganizationGrant numberCountry
David and Lucile Packard Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM115882-03 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: The structure of a virus-encoded nucleosome.
Authors: Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Miao Wang / Rachel Lee / Nikita Vasilyev / Jenny Zhang / Pablo De Ioannes / Bernard La Scola / Paul Talbert / Steve Henikoff / Evgeny ...Authors: Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Miao Wang / Rachel Lee / Nikita Vasilyev / Jenny Zhang / Pablo De Ioannes / Bernard La Scola / Paul Talbert / Steve Henikoff / Evgeny Nudler / Albert Erives / Karim-Jean Armache /
Abstract: Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to ...Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to the eukaryotic histone pairs H2B-H2A and H4-H3. These viral histones form 'forced' heterodimers, and a heterotetramer of four such heterodimers assembles DNA to form structures virtually identical to canonical eukaryotic nucleosomes.
History
DepositionFeb 24, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7lv8
  • Surface level: 7.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23529.png

Downloads & links

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Map

FileDownload / File: emd_23529.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Marseillevirus nucleosome, main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.4 / Movie #1: 7.4
Minimum - Maximum-17.334543 - 33.038497999999997
Average (Standard dev.)0.000058712118 (±1.000759)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z279.040279.040279.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-17.33533.0380.000

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Supplemental data

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Additional map: Unsharpened map of the structure of Marseillevirus nucleosome

Fileemd_23529_additional_1.map
AnnotationUnsharpened map of the structure of Marseillevirus nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A of the structure of Marseillevirus nucleosome

Fileemd_23529_half_map_1.map
AnnotationHalf-map A of the structure of Marseillevirus nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of the structure of Marseillevirus nucleosome

Fileemd_23529_half_map_2.map
AnnotationHalf-map B of the structure of Marseillevirus nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the Marseillevirus nucleosome

EntireName: Structure of the Marseillevirus nucleosome
Components
  • Complex: Structure of the Marseillevirus nucleosome
    • Protein or peptide: Histone doublet Delta-Gamma (Delta)
    • Protein or peptide: Histone doublet Delta-Gamma (Gamma)
    • Protein or peptide: Histone doublet Beta-Alpha (Beta)
    • Protein or peptide: Histone doublet Beta-Alpha (Alpha)
    • DNA: DNA (123-MER)
    • DNA: DNA (123-MER)

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Supramolecule #1: Structure of the Marseillevirus nucleosome

SupramoleculeName: Structure of the Marseillevirus nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: virus-encoded histone doublets Marseillevirus
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Histone doublet Delta-Gamma (Delta)

MacromoleculeName: Histone doublet Delta-Gamma (Delta) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marseillevirus marseillevirus
Molecular weightTheoretical: 10.462416 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LADHVSVGET QIPKASTQHL LRKAGSLSAA GDTEVPIRGF VHMKLHKLVQ KSLLAMQLAK RKTIMKSDVK KAAELMHLPV FAIPTKDSG AKGSVFLS

UniProtKB: Histone H3

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Macromolecule #2: Histone doublet Delta-Gamma (Gamma)

MacromoleculeName: Histone doublet Delta-Gamma (Gamma) / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marseillevirus marseillevirus
Molecular weightTheoretical: 11.7676 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
CRQKGAGSAG TGSETNSQEV RSQMRSTCLI IPKERFRTMA KEISKKEGHD VHIAEAALDM LQVIVESCTV RLLEKALVIT YSGKRTRVT SKDIETAFML EHGPLLE

UniProtKB: Histone H3

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Macromolecule #3: Histone doublet Beta-Alpha (Beta)

MacromoleculeName: Histone doublet Beta-Alpha (Beta) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marseillevirus marseillevirus
Molecular weightTheoretical: 11.228021 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MATQKETTRK RDKSVNFRLG LRNMLAQIHP DISVQTEALS ELSNIAVFLG KKISHGAVTL LPEGTKTIKS SAVLLAAGDL YGKDLGRHA VGEMTKAVTR YGSAK

UniProtKB: Histone H2B/H2A fusion protein

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Macromolecule #4: Histone doublet Beta-Alpha (Alpha)

MacromoleculeName: Histone doublet Beta-Alpha (Alpha) / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marseillevirus marseillevirus
Molecular weightTheoretical: 17.675625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ESKEGSRSSK AKLQISVARS ERLLREHGGC SRVSEGAAVA LAAAIEYFMG EVLELAGNAA RDSKKVRISV KHITLAIQND AALFAVVGK GVFSGAGVSL ISVPIPRKKA RKTTEKEASS PKKKAAPKKK KAASKQKKSL SDKELAKLTK KELAKYEKEQ G MSPGY

UniProtKB: Histone H2B/H2A fusion protein

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Macromolecule #5: DNA (123-MER)

MacromoleculeName: DNA (123-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 37.53091 KDa
SequenceString: (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) ...String:
(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) (DG)(DA) (DA)(DT)(DC)(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)

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Macromolecule #6: DNA (123-MER)

MacromoleculeName: DNA (123-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 37.152672 KDa
SequenceString: (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) ...String:
(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) (DG)(DA) (DT)(DT)(DC)(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)

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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

Concentration3.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHepesHepes
1.0 mMEDTAEDTA
2.0 mMDTTDTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4503 / Average exposure time: 2.5 sec. / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3017414
Startup modelType of model: OTHER / Details: Ab initio in CryoSparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 146506
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.15) / Details: Ab initio in CryoSparc
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1kx5

source_name: PDB, initial_model_type: experimental model

3lz0

chain_id: I, source_name: PDB, initial_model_type: experimental model

3lz0

chain_id: J, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7lv8:
Structure of the Marseillevirus nucleosome

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