+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22167 | |||||||||
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Title | Cryo-EM map of KSHV ORF68 | |||||||||
Map data | ORF68 | |||||||||
Sample |
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Function / homology | Herpesvirus major envelope glycoprotein / Herpesvirus putative major envelope glycoprotein / host cell cytoplasm / viral envelope / host cell nucleus / cytoplasm / Packaging protein UL32 Function and homology information | |||||||||
Biological species | Human gammaherpesvirus 8 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 Å | |||||||||
Authors | Didychuk AL / Gates SN / Martin A / Glaunsinger B | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2021 Title: A pentameric protein ring with novel architecture is required for herpesviral packaging. Authors: Allison L Didychuk / Stephanie N Gates / Matthew R Gardner / Lisa M Strong / Andreas Martin / Britt A Glaunsinger / Abstract: Genome packaging in large double-stranded DNA viruses requires a powerful molecular motor to force the viral genome into nascent capsids, which involves essential accessory factors that are poorly ...Genome packaging in large double-stranded DNA viruses requires a powerful molecular motor to force the viral genome into nascent capsids, which involves essential accessory factors that are poorly understood. Here, we present structures of two such accessory factors from the oncogenic herpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV; ORF68) and Epstein-Barr virus (EBV; BFLF1). These homologous proteins form highly similar homopentameric rings with a positively charged central channel that binds double-stranded DNA. Mutation of individual positively charged residues within but not outside the channel ablates DNA binding, and in the context of KSHV infection, these mutants fail to package the viral genome or produce progeny virions. Thus, we propose a model in which ORF68 facilitates the transfer of newly replicated viral genomes to the packaging motor. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22167.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-22167-v30.xml emd-22167.xml | 12 KB 12 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22167_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_22167.png | 162 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22167 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22167 | HTTPS FTP |
-Validation report
Summary document | emd_22167_validation.pdf.gz | 340 KB | Display | EMDB validaton report |
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Full document | emd_22167_full_validation.pdf.gz | 339.6 KB | Display | |
Data in XML | emd_22167_validation.xml.gz | 10.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22167 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22167 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22167.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ORF68 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pentamer structure of KSHV ORF68
Entire | Name: Pentamer structure of KSHV ORF68 |
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Components |
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-Supramolecule #1: Pentamer structure of KSHV ORF68
Supramolecule | Name: Pentamer structure of KSHV ORF68 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Human gammaherpesvirus 8 |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 536 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.25 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20.0 nm | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 2 second blot, 3 second wait. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 2408 / Average exposure time: 8.0 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |