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Yorodumi- EMDB-3236: Electron cryo-microscopy of filamentous flexible virus PepMV (Pep... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3236 | |||||||||
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Title | Electron cryo-microscopy of filamentous flexible virus PepMV (Pepino Mosaic Virus) | |||||||||
Map data | CryoEM map of PepMV, a Potexvirus. | |||||||||
Sample |
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Keywords | 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 / Coat protein Function and homology information | |||||||||
Biological species | Pepino mosaic virus | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Agirrezabala X / Mendez-Lopez E / Lasso G / Sanchez-Pina MA / Aranda MA / 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3236.map.gz | 7 MB | EMDB map data format | |
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Header (meta data) | emd-3236-v30.xml emd-3236.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | EMD-3236_pepmv_500.jpg | 700.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3236 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3236 | HTTPS FTP |
-Validation report
Summary document | emd_3236_validation.pdf.gz | 291 KB | Display | EMDB validaton report |
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Full document | emd_3236_full_validation.pdf.gz | 290.1 KB | Display | |
Data in XML | emd_3236_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3236 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3236 | HTTPS FTP |
-Related structure data
Related structure data | 5fn1MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3236.map.gz / Format: CCP4 / Size: 9.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of PepMV, a Potexvirus. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pepino Mosaic Virus, PepMV
Entire | Name: Pepino Mosaic Virus, PepMV |
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Components |
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-Supramolecule #1000: Pepino Mosaic Virus, PepMV
Supramolecule | Name: Pepino Mosaic Virus, PepMV / type: sample / ID: 1000 / Oligomeric state: Helical symmetry / Number unique components: 1 |
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Molecular weight | Theoretical: 35 MDa |
-Supramolecule #1: Pepino mosaic virus
Supramolecule | Name: Pepino mosaic virus / type: virus / ID: 1 / NCBI-ID: 112229 / Sci species name: Pepino mosaic virus / Sci species strain: PepMV-Sp13 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Solanum lycopersicum (tomato) / synonym: PLANTAE(HIGHER PLANTS) |
Host system | Organism: Nicotiana benthamiana (plant) |
Molecular weight | Theoretical: 35 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 / Details: 100 mM Tris-citric acid |
Grid | Details: Quantifoil R 2/2 holey carbon grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Feb 20, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 100 / Average electron dose: 25 e/Å2 Details: Every image is the average of 25 frames recorded by direct electron detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 102987 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Spring software used |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 3.95 Å Applied symmetry - Helical parameters - Δ&Phi: 41.1 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: Spring, EMAN2, CTFTILT |
CTF correction | Details: Each partcile phase flipping |