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- EMDB-23530: Marseillevirus heterotrimeric (hexameric) nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-23530
TitleMarseillevirus heterotrimeric (hexameric) nucleosome
Map data
SampleMarseillevirus heterotrimeric (hexameric) nucleosome:
(Histone doublet Delta-Gamma ...) x 2 / (Histone doublet Beta-Alpha ...) x 2 / (nucleic-acidNucleic acid) x 2
Function / homology
Function and homology information


nucleosome / protein heterodimerization activity / DNA binding
Similarity search - Function
Histone H2A / Histone 2A / 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: 4.5 Å
AuthorsValencia-Sanchez MI / Abini-Agbomson S / Armache K-J
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-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7lv9
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_23530.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 5.06 / Movie #1: 8
Minimum - Maximum-0.22592568 - 21.980764
Average (Standard dev.)-0.00028707556 (±1.0064764)
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-0.22621.981-0.000

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Supplemental data

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Half map: Half map A Structure of the Marseillevirus Hexamer

Fileemd_23530_half_map_1.map
AnnotationHalf map A Structure of the Marseillevirus Hexamer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map B Structure of the Marseillevirus Hexamer

Fileemd_23530_half_map_2.map
AnnotationHalf map B Structure of the Marseillevirus Hexamer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Marseillevirus heterotrimeric (hexameric) nucleosome

EntireName: Marseillevirus heterotrimeric (hexameric) nucleosome / Details: virus-encoded histone doublets Marseillevirus / Number of Components: 7

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Component #1: protein, Marseillevirus heterotrimeric (hexameric) nucleosome

ProteinName: Marseillevirus heterotrimeric (hexameric) nucleosome / Details: virus-encoded histone doublets Marseillevirus / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Histone doublet Delta-Gamma (Delta)

ProteinName: Histone doublet Delta-Gamma (Delta) / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.462416 kDa
SourceSpecies: Marseillevirus marseillevirus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Histone doublet Delta-Gamma (Gamma)

ProteinName: Histone doublet Delta-Gamma (Gamma) / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.7676 kDa
SourceSpecies: Marseillevirus marseillevirus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Histone doublet Beta-Alpha (Beta)

ProteinName: Histone doublet Beta-Alpha (Beta) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.228021 kDa
SourceSpecies: Marseillevirus marseillevirus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Histone doublet Beta-Alpha (Alpha)

ProteinName: Histone doublet Beta-Alpha (Alpha) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.675625 kDa
SourceSpecies: Marseillevirus marseillevirus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: nucleic-acid, DNA (96-MER)

nucleic acidName: DNA (96-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (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) ...Sequence:
(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)
MassTheoretical: 29.08757 kDa
SourceSpecies: synthetic construct (others)

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Component #7: nucleic-acid, DNA (96-MER)

nucleic acidName: DNA (96-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (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) ...Sequence:
(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)
MassTheoretical: 29.527826 kDa
SourceSpecies: synthetic construct (others)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 3.3 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 297 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 65 e/Å2 / Illumination Mode: OTHER
LensMagnification: 64000.0 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1000.0 - 2400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of Digital Images: 4503

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 128907
3D reconstructionAlgorithm: FOURIER SPACE / Software: cryoSPARC / Resolution: 4.5 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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