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Yorodumi- PDB-8ozp: In situ subtomogram average of Prototype Foamy Virus Env pentamer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ozp | ||||||
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Title | In situ subtomogram average of Prototype Foamy Virus Env pentamer of trimers | ||||||
Components | Envelope glycoprotein | ||||||
Keywords | VIRAL PROTEIN / membrane fusion / envelope glycoprotein / foamy virus / MPER / transmembrane / MEMBRANE PROTEIN | ||||||
Function / homology | CHOLESTEROL / PHOSPHATIDYLETHANOLAMINE Function and homology information | ||||||
Biological species | Eastern chimpanzee simian foamy virus | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 11.9 Å | ||||||
Authors | Calcraft, T. / Nans, A. / Rosenthal, P.B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cell / Year: 2024 Title: Integrated cryoEM structure of a spumaretrovirus reveals cross-kingdom evolutionary relationships and the molecular basis for assembly and virus entry. Authors: Thomas Calcraft / Nicole Stanke-Scheffler / Andrea Nans / Dirk Lindemann / Ian A Taylor / Peter B Rosenthal / Abstract: Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates ...Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates for gene and oncolytic therapies. Structural studies of PFV contribute to the understanding of the mechanisms of FV replication, cell entry and infection, and retroviral evolution. Here we combine cryoEM and cryoET to determine high-resolution in situ structures of the PFV icosahedral capsid (CA) and envelope glycoprotein (Env), including its type III transmembrane anchor and membrane-proximal external region (MPER), and show how they are organized in an integrated structure of assembled PFV particles. The atomic models reveal an ancient retroviral capsid architecture and an unexpected relationship between Env and other class 1 fusion proteins of the Mononegavirales. Our results represent the de novo structure determination of an assembled retrovirus particle. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ozp.cif.gz | 683.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ozp.ent.gz | 503.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ozp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ozp_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 8ozp_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 8ozp_validation.xml.gz | 81.1 KB | Display | |
Data in CIF | 8ozp_validation.cif.gz | 124 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/8ozp ftp://data.pdbj.org/pub/pdb/validation_reports/oz/8ozp | HTTPS FTP |
-Related structure data
Related structure data | 17317MC 8ozhC 8ozjC 8ozkC 8ozlC 8ozmC 8oznC 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 10 molecules ABDFHLEICG
#1: Protein | Mass: 113804.594 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern chimpanzee simian foamy virus / Gene: env / Production host: Homo sapiens (human) |
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-Sugars , 7 types, 33 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 6 molecules
#8: Chemical | #10: Chemical | |
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-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: subtomogram averaging |
-Sample preparation
Component | Name: Eastern chimpanzee simian foamy virus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT |
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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: 4500 nm / Nominal defocus min: 2000 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: 2.62 e/Å2 / Avg electron dose per subtomogram: 107.42 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 11.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2220 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 250 / Num. of volumes extracted: 156183 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 11.9→11.9 Å / Cor.coef. Fo:Fc: 0.991 / SU B: 776.699 / SU ML: 3.758 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: 439.565 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 22752 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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