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Yorodumi- PDB-8ozm: In situ cryoEM structure of the Prototype Foamy Virus capsid, hex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ozm | ||||||
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Title | In situ cryoEM structure of the Prototype Foamy Virus capsid, hexamer 1 localised reconstruction | ||||||
Components | Gag polyprotein | ||||||
Keywords | VIRAL PROTEIN / capsid / Gag / foamy virus / hexamer | ||||||
Function / homology | Function and homology information host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Eastern chimpanzee simian foamy virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Calcraft, T. / Nans, A. / Rosenthal, P.B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: In situ cryoEM structures of PFV Authors: Calcraft, T. / Lindemann, D. / Rosenthal, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ozm.cif.gz | 241.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ozm.ent.gz | 175.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ozm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ozm_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ozm_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ozm_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 8ozm_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/8ozm ftp://data.pdbj.org/pub/pdb/validation_reports/oz/8ozm | HTTPS FTP |
-Related structure data
Related structure data | 17314 17309 17311 17312 17313 17315 17316 17317 17318 17319 17320 17321 17322 8ozhC 8ozjC 8ozkC 8ozlC 8oznC 8ozpC 8ozqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 70693.414 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern chimpanzee simian foamy virus / Gene: gag / Production host: Homo sapiens (human) / References: UniProt: A0A1Q1N9V7 |
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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: Eastern chimpanzee simian foamy virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Eastern chimpanzee simian foamy virus |
Source (recombinant) | Organism: Homo sapiens (human) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK III / 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: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 |
-Processing
Software | Name: REFMAC / Version: 5.8.0352 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 52141 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 346237 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.4→3.4 Å / Cor.coef. Fo:Fc: 0.865 / SU B: 8.409 / SU ML: 0.133 / ESU R: 0.421 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 127.927 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 8052 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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