+Open data
-Basic information
Entry | Database: PDB / ID: 5fua | |||||||||
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Title | Cryo-EM of BK polyomavirus | |||||||||
Components | MAJOR CAPSID PROTEIN VP1 | |||||||||
Keywords | VIRUS / BKPYV / BK / POLYOMAVIRUS | |||||||||
Function / homology | Function and homology information caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | BK POLYOMAVIRUS | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||
Authors | Hurdiss, D.L. / Morgan, E.L. / Thompson, R.F. / Prescott, E.L. / Panou, M.M. / Macdonald, A. / Ranson, N.A. | |||||||||
Citation | Journal: Structure / Year: 2016 Title: New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy. Authors: Daniel L Hurdiss / Ethan L Morgan / Rebecca F Thompson / Emma L Prescott / Margarita M Panou / Andrew Macdonald / Neil A Ranson / Abstract: BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious ...BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious virions and VP1-only virus-like particles in cell culture, and determined their three-dimensional structures using cryo-electron microscopy (EM) and single-particle image processing. The resulting 7.6-Å resolution structure of BK and 9.1-Å resolution of the virus-like particles are the highest-resolution cryo-EM structures of any polyomavirus. These structures confirm that the architecture of the major structural protein components of these human polyomaviruses are similar to previous structures from other hosts, but give new insight into the location and role of the enigmatic minor structural proteins, VP2 and VP3. We also observe two shells of electron density, which we attribute to a structurally ordered part of the viral genome, and discrete contacts between this density and both VP1 and the minor capsid proteins. | |||||||||
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 | 5fua.cif.gz | 666.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fua.ent.gz | 540.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fua_validation.pdf.gz | 879.3 KB | Display | wwPDB validaton report |
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Full document | 5fua_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5fua_validation.xml.gz | 94.5 KB | Display | |
Data in CIF | 5fua_validation.cif.gz | 135.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/5fua ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fua | HTTPS FTP |
-Related structure data
Related structure data | 3283MC 3284C 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: 40154.617 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) BK POLYOMAVIRUS / Strain: DUNLOP / References: UniProt: P03088 |
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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 |
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Buffer solution | Name: 10MM HEPES PH 7.9, 1MM CACL2, 1MM MGCL2, 5MM KCL / pH: 7.9 / Details: 10MM HEPES PH 7.9, 1MM CACL2, 1MM MGCL2, 5MM KCL |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: 6.5 SECONDS BLOT BEFORE PLUNGING IN LIQUID ETHAN |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Dec 15, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 19000 X / Nominal defocus max: 4800 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Num. digital images: 432 |
-Processing
EM software | Name: RELION / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: CTFFIND3 | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 7.6 Å / Num. of particles: 2237 Details: A HOMOLOGY MODEL OF THE BKPYV VP1 ASYMMETRIC UNIT BASED ON THE CRYSTAL STRUCTURE OF SV40 (PDB 1SVA) WAS BUILT USING THE SWISS-MODEL SERVER. THIS WAS THEN FITTED (AS A RIGID BODY) INTO A ...Details: A HOMOLOGY MODEL OF THE BKPYV VP1 ASYMMETRIC UNIT BASED ON THE CRYSTAL STRUCTURE OF SV40 (PDB 1SVA) WAS BUILT USING THE SWISS-MODEL SERVER. THIS WAS THEN FITTED (AS A RIGID BODY) INTO A CORRESPONDING SEGMENT OF THE BKPYV CRYO-EM DENSITY MAP GENERATED USING UCSF CHIMERA. FLEXIBLE FITTING OF THE HOMOLOGY MODEL WAS THEN CARRIED OUT USING MDFF (TRABUCO ET AL. 10 2008). SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3283. (DEPOSITION ID: 14117). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Details: REFINEMENT PROTOCOL--HOMOLOGY MODEL | ||||||||||||
Refinement | Highest resolution: 7.6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.6 Å
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