+Open data
-Basic information
Entry | Database: PDB / ID: 6esb | |||||||||
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Title | BK polyomavirus + 20 mM GT1b oligosaccharide | |||||||||
Components |
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Keywords | VIRUS / Polyomavirus / Receptor / Complex / Glycan | |||||||||
Function / homology | Function and homology information caveolin-mediated endocytosis of virus by host cell / : / : / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=7 icosahedral viral capsid / viral penetration into host nucleus / viral capsid / protein complex oligomerization / monoatomic ion channel activity ...caveolin-mediated endocytosis of virus by host cell / : / : / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=7 icosahedral viral capsid / viral penetration into host nucleus / viral capsid / protein complex oligomerization / monoatomic ion channel activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding Similarity search - Function | |||||||||
Biological species | BK polyomavirus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Hurdiss, D.L. / Ranson, N.A. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2018 Title: The Structure of an Infectious Human Polyomavirus and Its Interactions with Cellular Receptors. Authors: Daniel L Hurdiss / Martin Frank / Joseph S Snowden / Andrew Macdonald / Neil A Ranson / Abstract: BK polyomavirus (BKV) causes polyomavirus-associated nephropathy and hemorrhagic cystitis in immunosuppressed patients. These are diseases for which we currently have limited treatment options, but ...BK polyomavirus (BKV) causes polyomavirus-associated nephropathy and hemorrhagic cystitis in immunosuppressed patients. These are diseases for which we currently have limited treatment options, but potential therapies could include pre-transplant vaccination with a multivalent BKV vaccine or therapeutics which inhibit capsid assembly or block attachment and entry into target cells. A useful tool in such efforts would be a high-resolution structure of the infectious BKV virion and how this interacts with its full repertoire of cellular receptors. We present the 3.4-Å cryoelectron microscopy structure of native, infectious BKV in complex with the receptor fragment of GT1b ganglioside. We also present structural evidence that BKV can utilize glycosaminoglycans as attachment receptors. This work highlights features that underpin capsid stability and provides a platform for rational design and development of urgently needed pharmacological interventions for BKV-associated diseases. | |||||||||
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 | 6esb.cif.gz | 365.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6esb.ent.gz | 301 KB | Display | PDB format |
PDBx/mmJSON format | 6esb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6esb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6esb_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6esb_validation.xml.gz | 69 KB | Display | |
Data in CIF | 6esb_validation.cif.gz | 103.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/6esb ftp://data.pdbj.org/pub/pdb/validation_reports/es/6esb | HTTPS FTP |
-Related structure data
Related structure data | 3944MC 3945C 3946C 4212C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 40053.449 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) BK polyomavirus / Cell line: Vero / References: UniProt: Q65613, UniProt: P03088*PLUS #2: Protein | | Mass: 38252.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BK polyomavirus / Cell line: Vero / References: UniProt: P03094 #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CA / |
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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: BK polyomavirus / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Human polyomavirus 1 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Virus shell | Name: Icosahedron / Diameter: 500 nm / Triangulation number (T number): 7 |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.25 mg/ml / 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 FIELD |
Image recording | Electron dose: 59 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: I (icosahedral) |
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40334 / Symmetry type: POINT |