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Open data
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Basic information
Entry | Database: PDB / ID: 4v7q | ||||||||||||
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Title | Atomic model of an infectious rotavirus particle | ||||||||||||
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![]() | VIRUS / Rotavirus / Triple Layered Particle / Near Atomic Resolution / VP2 / VP6 / VP4 / VP7 / Double layered particle / de novo / Infectious / DLP / ICOSAHEDRAL VIRUS | ||||||||||||
Function / homology | ![]() viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / host cell rough endoplasmic reticulum / viral inner capsid / 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 ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / host cell rough endoplasmic reticulum / viral inner capsid / 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 / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / RNA binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
![]() | Settembre, E.C. / Chen, J.Z. / Dormitzer, P.R. / Grigorieff, N. / Harrison, S.C. | ||||||||||||
![]() | ![]() Title: Atomic model of an infectious rotavirus particle. Authors: Ethan C Settembre / James Z Chen / Philip R Dormitzer / Nikolaus Grigorieff / Stephen C Harrison / ![]() Abstract: Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling ...Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus-penetration protein, and infectivity analyses of structure-based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single-particle analysis at about 4.3 Å resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8(*) and VP5(*)) retain their association after proteolytic cleavage, reveals multiple structural roles for the β-barrel domain of VP5(*), and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 478.2 KB | Display | |
Data in CIF | ![]() | 664.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5199MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
-Protein , 4 types, 31 molecules AAABACADAEAFAGAHAIAJAKALAMANAOBABFBGBHBIBJBKBLBMBNBOBPBQBXBYBZ
#1: Protein | Mass: 93190.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 44934.766 Da / Num. of mol.: 13 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 31232.234 Da / Num. of mol.: 13 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | Mass: 86655.586 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 2 types, 8 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #7: Sugar | ChemComp-NAG / | |
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-Non-polymers , 1 types, 5 molecules ![](data/chem/img/ZN.gif)
#6: Chemical | ChemComp-ZN / |
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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 |
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Sample preparation
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Details of virus | Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION | |||||||||||||||
Natural host | Organism: Macaca mulatta / Strain: Monkey Kidney Cells | |||||||||||||||
Buffer solution | Name: 20 mM Tris / pH: 7.5 / Details: 20 mM Tris | |||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: in normal coldroom environment, ETHANE, manual plunger, front blotting for 3s before plunging, temperature 90 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Mar 1, 2008 Details: Cut-plate film holders to reduce electron back-scattering |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 56772 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm |
Specimen holder | Temperature: 90 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
CTF correction | Details: individual particle | ||||||||||||
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Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: projection matching / Resolution: 3.8 Å / Num. of particles: 4187 / Details: icosahedral (I2) averaging / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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