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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24238 | |||||||||
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Title | Melbournevirus nucleosome like particle | |||||||||
![]() | Melbournevirus nucleosome like particle | |||||||||
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![]() | nucleosome / Virus / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.89 Å | |||||||||
![]() | Liu Y / Toner CM | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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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 | ![]() | 2.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.7 KB 14.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 22.3 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 5.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n8nMC M: atomic model generated by this map C: citing same article ( |
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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
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Annotation | Melbournevirus nucleosome like particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Melbournevirus nucleosome like particle
Entire | Name: Melbournevirus nucleosome like particle |
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Components |
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-Supramolecule #1: Melbournevirus nucleosome like particle
Supramolecule | Name: Melbournevirus nucleosome like particle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 218 KDa |
-Supramolecule #2: Histone H4-H3 doublet, Histone H2B-H2A doublet
Supramolecule | Name: Histone H4-H3 doublet, Histone H2B-H2A doublet / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: DNA 147-mer
Supramolecule | Name: DNA 147-mer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Histone H4-H3 doublet
Macromolecule | Name: Histone H4-H3 doublet / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.73718 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 H3-like protein |
-Macromolecule #2: Histone H2B-H2A doublet
Macromolecule | Name: Histone H2B-H2A doublet / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 32.05816 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 H2B/H2A fusion protein |
-Macromolecule #3: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.153781 KDa |
Sequence | 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) ...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) |
-Macromolecule #4: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.594043 KDa |
Sequence | 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) ...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) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 |
Vitrification | Cryogen name: ETHANE |
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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) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |