+Open data
-Basic information
Entry | Database: PDB / ID: 4v7q | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Atomic model of an infectious rotavirus particle | ||||||||||||
Components |
| ||||||||||||
Keywords | VIRUS / Rotavirus / Triple Layered Particle / Near Atomic Resolution / VP2 / VP6 / VP4 / VP7 / Double layered particle / de novo / Infectious / DLP / ICOSAHEDRAL VIRUS | ||||||||||||
Function / homology | Function and homology information viral intermediate capsid / host cell endoplasmic reticulum lumen / T=2 icosahedral viral capsid / host cell rough endoplasmic reticulum / T=13 icosahedral viral capsid / viral inner capsid / permeabilization of host organelle membrane involved in viral entry into host cell / host cytoskeleton / viral outer capsid / host cell endoplasmic reticulum-Golgi intermediate compartment ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=2 icosahedral viral capsid / host cell rough endoplasmic reticulum / T=13 icosahedral viral capsid / viral inner capsid / permeabilization of host organelle membrane involved in viral entry into host cell / host cytoskeleton / viral outer capsid / 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 | Simian rotavirus A Rhesus rotavirus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Settembre, E.C. / Chen, J.Z. / Dormitzer, P.R. / Grigorieff, N. / Harrison, S.C. | ||||||||||||
Citation | Journal: EMBO J / Year: 2011 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v7q.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4v7q.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v7q_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4v7q_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 4v7q_validation.xml.gz | 477.7 KB | Display | |
Data in CIF | 4v7q_validation.cif.gz | 664.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/4v7q ftp://data.pdbj.org/pub/pdb/validation_reports/v7/4v7q | HTTPS FTP |
-Related structure data
Related structure data | 5199MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-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.) Simian rotavirus A / Strain: RRV / Gene: Rotavirus / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: B3F2X3 #2: Protein | Mass: 44934.766 Da / Num. of mol.: 13 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhesus rotavirus / Strain: RRV / Gene: Rotavirus / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: B2BN53 #3: Protein | Mass: 31232.234 Da / Num. of mol.: 13 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian rotavirus A / Strain: RRV / Cell (production host): KIDNEY CELLS / Organ (production host): KIDNEY / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: C3RX25, UniProt: P12476*PLUS #4: 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 (production host): KIDNEY CELLS / Organ (production host): KIDNEY / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: C3RX20 |
---|
-Sugars , 2 types, 8 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #7: Sugar | ChemComp-NAG / | |
---|
-Non-polymers , 1 types, 5 molecules
#6: Chemical | ChemComp-ZN / |
---|
-Details
Has protein modification | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F30 / Date: Mar 1, 2008 Details: Cut-plate film holders to reduce electron back-scattering |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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 |
-Processing
CTF correction | Details: individual particle | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|