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Yorodumi- EMDB-24687: Cryo-EM structure of bluetongue virus capsid protein at low endos... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24687 | |||||||||
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Title | Cryo-EM structure of bluetongue virus capsid protein at low endosomal pH intermediate state 3 | |||||||||
Map data | IMS3 | |||||||||
Sample |
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Function / homology | Outer capsid protein VP5, Orbivirus / Orbivirus outer capsid protein VP5 / viral capsid / structural molecule activity / Outer capsid protein VP5 Function and homology information | |||||||||
Biological species | Bluetongue virus (serotype 1 / isolate South Africa) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Xia X / Wu WN / Cui YX / Roy P / Zhou ZH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Microbiol / Year: 2021 Title: Bluetongue virus capsid protein VP5 perforates membranes at low endosomal pH during viral entry. Authors: Xian Xia / Weining Wu / Yanxiang Cui / Polly Roy / Z Hong Zhou / Abstract: Bluetongue virus (BTV) is a non-enveloped virus and causes substantial morbidity and mortality in ruminants such as sheep. Fashioning a receptor-binding protein (VP2) and a membrane penetration ...Bluetongue virus (BTV) is a non-enveloped virus and causes substantial morbidity and mortality in ruminants such as sheep. Fashioning a receptor-binding protein (VP2) and a membrane penetration protein (VP5) on the surface, BTV releases its genome-containing core (VP3 and VP7) into the host cell cytosol after perforation of the endosomal membrane. Unlike enveloped ones, the entry mechanisms of non-enveloped viruses into host cells remain poorly understood. Here we applied single-particle cryo-electron microscopy, cryo-electron tomography and structure-guided functional assays to characterize intermediate states of BTV cell entry in endosomes. Four structures of BTV at the resolution range of 3.4-3.9 Å show the different stages of structural rearrangement of capsid proteins on exposure to low pH, including conformational changes of VP5, stepwise detachment of VP2 and a small shift of VP7. In detail, sensing of the low-pH condition by the VP5 anchor domain triggers three major VP5 actions: projecting the hidden dagger domain, converting a surface loop to a protonated β-hairpin that anchors VP5 to the core and stepwise refolding of the unfurling domains into a six-helix stalk. Cryo-electron tomography structures of BTV interacting with liposomes show a length decrease of the VP5 stalk from 19.5 to 15.5 nm after its insertion into the membrane. Our structures, functional assays and structure-guided mutagenesis experiments combined indicate that this stalk, along with dagger domain and the WHXL motif, creates a single pore through the endosomal membrane that enables the viral core to enter the cytosol. Our study unveils the detailed mechanisms of BTV membrane penetration and showcases general methods to study cell entry of other non-enveloped viruses. | |||||||||
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_24687.map.gz | 94 MB | EMDB map data format | |
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Header (meta data) | emd-24687-v30.xml emd-24687.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_24687.png | 163.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24687 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24687 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24687.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | IMS3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 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 : Bluetongue virus (serotype 1 / isolate South Africa)
Entire | Name: Bluetongue virus (serotype 1 / isolate South Africa) |
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Components |
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-Supramolecule #1: Bluetongue virus (serotype 1 / isolate South Africa)
Supramolecule | Name: Bluetongue virus (serotype 1 / isolate South Africa) / type: virus / ID: 1 / Parent: 0 Details: The virus was generated from BHK-21 cell and purified by sucrose gradient. NCBI-ID: 10905 Sci species name: Bluetongue virus (serotype 1 / isolate South Africa) Sci species strain: BTV-1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: sheep (sheep) |
Virus shell | Shell ID: 1 / Diameter: 880.0 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5.5 / Component - Concentration: 20.0 mM / Component - Name: sodium citrate |
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 3609 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 913440 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Number classes: 5 / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 120974 |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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