+Open data
-Basic information
Entry | Database: PDB / ID: 7thx | ||||||
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Title | Cryo-EM structure of W6 possum enterovirus | ||||||
Components | (Capsid protein ...) x 4 | ||||||
Keywords | VIRUS / enterovirus / icosahedral | ||||||
Function / homology | : / SPHINGOSINE Function and homology information | ||||||
Biological species | Possum enterovirus W6 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å | ||||||
Authors | Wang, I. / Jayawardena, N. / Strauss, M. / Bostina, M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Viruses / Year: 2022 Title: Cryo-EM Structure of a Possum Enterovirus. Authors: Ivy Wang / Sandeep K Gupta / Guillaume Ems / Nadishka Jayawardena / Mike Strauss / Mihnea Bostina / Abstract: Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess ...Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess the structural diversity of these picornaviruses. The capsid structure, determined to ~3 Å resolution by single particle analysis, exhibits a largely smooth surface, similar to EV-F3 (formerly BEV-2). Although the cellular receptor is not known, the absence of charged residues on the outer surface of the canyon suggest a different receptor type than for EV-F3. Density for the pocket factor is clear, with the entrance to the pocket being smaller than for other enteroviruses. | ||||||
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 | 7thx.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7thx.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 7thx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7thx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7thx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7thx_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 7thx_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/7thx ftp://data.pdbj.org/pub/pdb/validation_reports/th/7thx | HTTPS FTP |
-Related structure data
Related structure data | 25905MC 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
-Capsid protein ... , 4 types, 4 molecules 1234
#1: Protein | Mass: 30311.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Possum enterovirus W6 |
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#2: Protein | Mass: 26577.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Possum enterovirus W6 |
#3: Protein | Mass: 26997.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Possum enterovirus W6 |
#4: Protein | Mass: 7632.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Possum enterovirus W6 |
-Non-polymers , 3 types, 23 molecules
#5: Chemical | ChemComp-SPH / |
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#6: Chemical | ChemComp-K / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: Enterovirus / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL |
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Source (natural) | Organism: Possum enterovirus W6 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Possum enterovirus W6 |
Buffer solution | pH: 7.4 |
Specimen | 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 / Nominal defocus max: 3000 nm / Nominal defocus min: 750 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.37 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9687 / Details: relion 3.1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OSN Accession code: 5OSN / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.96→114.838 Å / Cor.coef. Fo:Fc: 0.745 / WRfactor Rwork: 0.271 / SU B: 13.188 / SU ML: 0.224 / Average fsc overall: 0.9236 / Average fsc work: 0.9236 / ESU R: 0.321 Details: Hydrogens have been added in their riding positions
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Solvent computation | Solvent model: BABINET MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.726 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 37770 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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