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Yorodumi- PDB-8uk2: The rotavirus VP5*/VP8* conformational transition permeabilizes m... -
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-Basic information
Entry | Database: PDB / ID: 8uk2 | ||||||
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Title | The rotavirus VP5*/VP8* conformational transition permeabilizes membranes to Ca2+ (class 5 reconstruction) | ||||||
Components |
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Keywords | VIRAL PROTEIN / Non-enveloped virus / viral particle / entry / membrane-penetration / rotavirus / VP4 / VP5* / VP8* / calcium / Ca2+ / liposome | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / receptor-mediated virion attachment to host cell / virion attachment to host cell ...host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / receptor-mediated virion attachment to host cell / virion attachment to host cell / host cell plasma membrane / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Simian rotavirus A strain RRV | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å | ||||||
Authors | De Sautu, M. / Herrmann, T. / Jenni, S. / Harrison, S.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: PLoS Pathog / Year: 2024 Title: The rotavirus VP5*/VP8* conformational transition permeabilizes membranes to Ca2. Authors: Marilina de Sautu / Tobias Herrmann / Gustavo Scanavachi / Simon Jenni / Stephen C Harrison / Abstract: Rotaviruses infect cells by delivering into the cytosol a transcriptionally active inner capsid particle (a "double-layer particle": DLP). Delivery is the function of a third, outer layer, which ...Rotaviruses infect cells by delivering into the cytosol a transcriptionally active inner capsid particle (a "double-layer particle": DLP). Delivery is the function of a third, outer layer, which drives uptake from the cell surface into small vesicles from which the DLPs escape. In published work, we followed stages of rhesus rotavirus (RRV) entry by live-cell imaging and correlated them with structures from cryogenic electron microscopy and tomography (cryo-EM and cryo-ET). The virus appears to wrap itself in membrane, leading to complete engulfment and loss of Ca2+ from the vesicle produced by the wrapping. One of the outer-layer proteins, VP7, is a Ca2+-stabilized trimer; loss of Ca2+ releases both VP7 and the other outer-layer protein, VP4, from the particle. VP4, activated by cleavage into VP8* and VP5*, is a trimer that undergoes a large-scale conformational rearrangement, reminiscent of the transition that viral fusion proteins undergo to penetrate a membrane. The rearrangement of VP5* thrusts a 250-residue, C-terminal segment of each of the three subunits outward, while allowing the protein to remain attached to the virus particle and to the cell being infected. We proposed that this segment inserts into the membrane of the target cell, enabling Ca2+ to cross. In the work reported here, we show the validity of key aspects of this proposed sequence. By cryo-EM studies of liposome-attached virions ("triple-layer particles": TLPs) and single-particle fluorescence imaging of liposome-attached TLPs, we confirm insertion of the VP4 C-terminal segment into the membrane and ensuing generation of a Ca2+ "leak". The results allow us to formulate a molecular description of early events in entry. We also discuss our observations in the context of other work on double-strand RNA virus entry. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uk2.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8uk2.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8uk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/8uk2 ftp://data.pdbj.org/pub/pdb/validation_reports/uk/8uk2 | HTTPS FTP |
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-Related structure data
Related structure data | 42343MC 8uk3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 86655.586 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian rotavirus A strain RRV / Cell line (production host): MA104 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: G0YZG6 #2: Protein | Mass: 37136.531 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian rotavirus A strain RRV / Cell line (production host): MA104 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P12476 #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-CA / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Simian rotavirus A strain RRV / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Simian rotavirus A strain RRV |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 8 Å / Resolution method: OTHER / Num. of particles: 56593 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |
Atomic model building | PDB-ID: 6WXG Accession code: 6WXG / Source name: PDB / Type: experimental model |