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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23530 | |||||||||
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Title | Marseillevirus heterotrimeric (hexameric) nucleosome | |||||||||
![]() | Structure of the Marseillevirus Hexamer | |||||||||
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Function / homology | ![]() structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding Similarity search - Function | |||||||||
Biological species | synthetic construct (others) / ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Valencia-Sanchez MI / Abini-Agbomson S / Armache K-J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 22.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.8 KB 23.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 198.7 KB | ||
Others | ![]() ![]() | 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lv9MC ![]() 7lv8C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the Marseillevirus Hexamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map A Structure of the Marseillevirus Hexamer
File | emd_23530_half_map_1.map | ||||||||||||
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Annotation | Half map A Structure of the Marseillevirus Hexamer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B Structure of the Marseillevirus Hexamer
File | emd_23530_half_map_2.map | ||||||||||||
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Annotation | Half map B Structure of the Marseillevirus Hexamer | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Marseillevirus heterotrimeric (hexameric) nucleosome
Entire | Name: Marseillevirus heterotrimeric (hexameric) nucleosome |
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Components |
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-Supramolecule #1: Marseillevirus heterotrimeric (hexameric) nucleosome
Supramolecule | Name: Marseillevirus heterotrimeric (hexameric) nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: virus-encoded histone doublets Marseillevirus |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Histone doublet Delta-Gamma (Delta)
Macromolecule | Name: Histone doublet Delta-Gamma (Delta) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.462416 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: LADHVSVGET QIPKASTQHL LRKAGSLSAA GDTEVPIRGF VHMKLHKLVQ KSLLAMQLAK RKTIMKSDVK KAAELMHLPV FAIPTKDSG AKGSVFLS |
-Macromolecule #2: Histone doublet Delta-Gamma (Gamma)
Macromolecule | Name: Histone doublet Delta-Gamma (Gamma) / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.7676 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: CRQKGAGSAG TGSETNSQEV RSQMRSTCLI IPKERFRTMA KEISKKEGHD VHIAEAALDM LQVIVESCTV RLLEKALVIT YSGKRTRVT SKDIETAFML EHGPLLE |
-Macromolecule #3: Histone doublet Beta-Alpha (Beta)
Macromolecule | Name: Histone doublet Beta-Alpha (Beta) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.228021 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MATQKETTRK RDKSVNFRLG LRNMLAQIHP DISVQTEALS ELSNIAVFLG KKISHGAVTL LPEGTKTIKS SAVLLAAGDL YGKDLGRHA VGEMTKAVTR YGSAK |
-Macromolecule #4: Histone doublet Beta-Alpha (Alpha)
Macromolecule | Name: Histone doublet Beta-Alpha (Alpha) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 17.675625 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: ESKEGSRSSK AKLQISVARS ERLLREHGGC SRVSEGAAVA LAAAIEYFMG EVLELAGNAA RDSKKVRISV KHITLAIQND AALFAVVGK GVFSGAGVSL ISVPIPRKKA RKTTEKEASS PKKKAAPKKK KAASKQKKSL SDKELAKLTK KELAKYEKEQ G MSPGY |
-Macromolecule #5: DNA (96-MER)
Macromolecule | Name: DNA (96-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 29.08757 KDa |
Sequence | String: (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) ...String: (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) |
-Macromolecule #6: DNA (96-MER)
Macromolecule | Name: DNA (96-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 29.527826 KDa |
Sequence | 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) ...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) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.3 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 stage | Specimen 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
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7lv9: |