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Yorodumi- PDB-5fn1: Electron cryo-microscopy of filamentous flexible virus PepMV (Pep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fn1 | ||||||
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Title | Electron cryo-microscopy of filamentous flexible virus PepMV (Pepino Mosaic Virus) | ||||||
Components |
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Keywords | VIRUS / PEPMV / FILAMENTOUS PLANT VIRUS / POTEXVIRUS / HELICAL SYMMETRY | ||||||
Function / homology | Potexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein / viral capsid / structural molecule activity / RNA / Coat protein Function and homology information | ||||||
Biological species | PEPINO MOSAIC VIRUS | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Agirrezabala, X. / Mendez-Lopez, E. / Lasso, G. / Sanchez-Pina, M.A. / Aranda, M.A. / Valle, M. | ||||||
Citation | Journal: Elife / Year: 2015 Title: The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses. Authors: Xabier Agirrezabala / Eduardo Méndez-López / Gorka Lasso / M Amelia Sánchez-Pina / Miguel Aranda / Mikel Valle / Abstract: Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We ...Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We describe here a structure at 3.9 Å resolution, from electron cryomicroscopy, of Pepino mosaic virus (PepMV), a representative of the genus Potexvirus (family Alphaflexiviridae). Our results allow modeling of the CP and its interactions with viral RNA. The overall fold of PepMV CP resembles that of nucleoproteins (NPs) from the genus Phlebovirus (family Bunyaviridae), a group of enveloped (-)ssRNA viruses. The main difference between potexvirus CP and phlebovirus NP is in their C-terminal extensions, which appear to determine the characteristics of the distinct multimeric assemblies - a flexuous, helical rod or a loose ribonucleoprotein. The homology suggests gene transfer between eukaryotic (+) and (-)ssRNA viruses. | ||||||
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 | 5fn1.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fn1.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/5fn1 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/5fn1 | HTTPS FTP |
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-Related structure data
Related structure data | 3236MC 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 | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 18 / Rise per n subunits: 3.95 Å / Rotation per n subunits: -41.1 °) |
-Components
#1: Protein | Mass: 25146.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PEPINO MOSAIC VIRUS / Strain: PEPMV-SP13 / References: UniProt: Q71FK2 |
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#2: RNA chain | Mass: 1485.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PEPINO MOSAIC VIRUS / Strain: PEPMV-SP13 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Pepino Mosaic Virus, PepMV / Type: VIRUS |
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Buffer solution | Name: 100 MM TRIS-CITRIC ACID / pH: 8 / Details: 100 MM TRIS-CITRIC ACID |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK II, |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Feb 20, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 102987 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 100 |
-Processing
EM software |
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CTF correction | Details: EACH PARTICLE PHASE FLIPPING | ||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Actual pixel size: 1.36 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3236. (DEPOSITION ID: 14021). Symmetry type: HELICAL | ||||||||||||||||
Refinement | Highest resolution: 3.9 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.9 Å
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