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Yorodumi- PDB-3iyk: Bluetongue virus structure reveals a sialic acid binding domain, ... -
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-Basic information
Entry | Database: PDB / ID: 3iyk | ||||||
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Title | Bluetongue virus structure reveals a sialic acid binding domain, amphipathic helices and a central coiled coil in the outer capsid proteins | ||||||
Components |
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Keywords | VIRUS / Icosahedral virus | ||||||
Function / homology | Function and homology information virion component => GO:0044423 / viral capsid / structural molecule activity Similarity search - Function | ||||||
Biological species | Bluetongue virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å | ||||||
Authors | Zhang, X. / Boyce, M. / Bhattacharya, B. / Zhang, X. / Schein, S. / Roy, P. / Zhou, Z.H. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2010 Title: Bluetongue virus coat protein VP2 contains sialic acid-binding domains, and VP5 resembles enveloped virus fusion proteins. Authors: Xing Zhang / Mark Boyce / Bishnupriya Bhattacharya / Xiaokang Zhang / Stan Schein / Polly Roy / Z Hong Zhou / Abstract: Bluetongue virus (BTV) is transmitted by blood-feeding insects (Culicoides sp.) and causes hemorrhagic diseases in livestock. BTV is a nonenveloped, double-stranded RNA (dsRNA) virus with two capsids: ...Bluetongue virus (BTV) is transmitted by blood-feeding insects (Culicoides sp.) and causes hemorrhagic diseases in livestock. BTV is a nonenveloped, double-stranded RNA (dsRNA) virus with two capsids: a well-studied, stable core enclosing the dsRNA genome and a highly unstable, poorly studied coat responsible for host cell attachment and entry. Here, based on cryo-electron microscopy (cryoEM), we report a 7-A resolution structure of the infectious BTV virion, including the coat proteins. We show that unlike other dsRNA viruses, the VP2 attachment trimer has a triskelion shape composed of three tip domains branching from a central hub domain. We identify three putative sialic acid-binding pockets in the hub and present supporting biochemical data indicating sugar moiety binding is important for BTV infection. Despite being a nonenveloped virus, the putative VP5 membrane penetration trimer, located slightly inward of the VP2 attachment trimer, has a central coiled-coil alpha-helical bundle, similar to the fusion proteins of many enveloped viruses (e.g., HIV, herpesviruses, vesicular stomatitis virus, and influenza virus). Moreover, mapping of the amino acid sequence of VP5 to the secondary structural elements identified by cryoEM locates 15 amphipathic alpha-helical regions on the external surface of each VP5 trimer. The cryoEM density map also reveals few, weak interactions between the VP5 trimer and both the outer-coat VP2 trimer and the underlying core VP7 trimer, suggesting that the surface of VP5 could unfurl like an umbrella during penetration and shedding of the coat to release the transcriptionally active core particle. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3iyk.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iyk.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 3iyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/3iyk ftp://data.pdbj.org/pub/pdb/validation_reports/iy/3iyk | HTTPS FTP |
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-Related structure data
Related structure data | 5147MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 59070.371 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bluetongue virus / References: UniProt: C5IWW1 #2: Protein | Mass: 70499.766 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bluetongue virus / References: UniProt: C5IWV8 #3: Sugar | |
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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: Bluetongue VirusBluetongue disease / Type: VIRUS / Details: Icosahedron. The sample was monodisperse in ice |
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Details of virus | Empty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Bos taurus |
Buffer solution | pH: 8 / Details: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: PBS |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 90 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 80000 X / Calibrated magnification: 79787 X / Cs: 2 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Gatan 626 / Temperature: 90 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GENERIC CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Each particle | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: projection matching / Resolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3400 / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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