+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3785 | |||||||||
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Title | Structure of Watermelon mosaic virus potyvirus. | |||||||||
Map data | Cryoelectron microscopy map of Watermelon mosaic virus filament. Resulting map from Relion postprocessing. | |||||||||
Sample |
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Keywords | filamentous virus / potyvirus / plant pathogen / virus | |||||||||
Function / homology | Potyvirus coat protein / Potyvirus coat protein / viral capsid / Coat protein Function and homology information | |||||||||
Biological species | Watermelon mosaic virus | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Zamora M / Mendez-Lopez E | |||||||||
Funding support | Spain, 1 items
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Citation | Journal: Sci Adv / Year: 2017 Title: Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses. Authors: Miguel Zamora / Eduardo Méndez-López / Xabier Agirrezabala / Rebeca Cuesta / José L Lavín / M Amelia Sánchez-Pina / Miguel A Aranda / Mikel Valle / Abstract: Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. ...Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. Infective potyvirus virions are long flexuous filaments where coat protein (CP) subunits assemble in helical mode bound to a monopartite positive-sense single-stranded RNA [(+)ssRNA] genome. We present the cryo-electron microscopy (cryoEM) structure of the potyvirus watermelon mosaic virus at a resolution of 4.0 Å. The atomic model shows a conserved fold for the CPs of flexible filamentous plant viruses, including a universally conserved RNA binding pocket, which is a potential target for antiviral compounds. This conserved fold of the CP is widely distributed in eukaryotic viruses and is also shared by nucleoproteins of enveloped viruses with segmented (-)ssRNA (negative-sense ssRNA) genomes, including influenza 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_3785.map.gz | 42.6 MB | EMDB map data format | |
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Header (meta data) | emd-3785-v30.xml emd-3785.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3785_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_3785.png | 245.2 KB | ||
Filedesc metadata | emd-3785.cif.gz | 5.4 KB | ||
Others | emd_3785_additional.map.gz emd_3785_half_map_1.map.gz emd_3785_half_map_2.map.gz | 17.4 MB 35.5 MB 35.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3785 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3785 | HTTPS FTP |
-Related structure data
Related structure data | 5odvMC 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_3785.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryoelectron microscopy map of Watermelon mosaic virus filament. Resulting map from Relion postprocessing. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryoelectron microscopy map of Watermelon mosaic virus filament....
File | emd_3785_additional.map | ||||||||||||
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Annotation | Cryoelectron microscopy map of Watermelon mosaic virus filament. Map generated by applying helical symmetry parameters to Relion postprocessing resulting map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half 1 map of Watermelon mosaic virus...
File | emd_3785_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half 1 map of Watermelon mosaic virus filament resulting from Relion 3D Refine. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half 2 map of Watermelon mosaic virus...
File | emd_3785_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half 2 map of Watermelon mosaic virus filament resulting from Relion 3D Refine. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Watermelon mosaic virus
Entire | Name: Watermelon mosaic virus |
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Components |
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-Supramolecule #1: Watermelon mosaic virus
Supramolecule | Name: Watermelon mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 146500 / Sci species name: Watermelon mosaic virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: coat protein
Macromolecule | Name: coat protein / type: protein_or_peptide / ID: 1 Details: 57 residues from N-terminus and 17 residues from C-terminus are not present in our pdb model due to the absence of densities for them in the cryo-electron microscopy map as a consequence of ...Details: 57 residues from N-terminus and 17 residues from C-terminus are not present in our pdb model due to the absence of densities for them in the cryo-electron microscopy map as a consequence of being high flexible regions in the protein. Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Watermelon mosaic virus |
Molecular weight | Theoretical: 31.463412 KDa |
Sequence | String: SGKEAVENLD AGKESKKDTS GKGDKPQNSQ TGQGSKEQTK TGTVSKDVNV GSKGKEVPRL QKITKKMNLP TVGGKIILSL DHLLEYKPN QVDLFNTRAT KTQFESWYSA VKVEYDLNDE QMGVIMNGFM VWCIDNGTSP DVNGVWVMMD GEEQVEYPLK P IVENAKPT ...String: SGKEAVENLD AGKESKKDTS GKGDKPQNSQ TGQGSKEQTK TGTVSKDVNV GSKGKEVPRL QKITKKMNLP TVGGKIILSL DHLLEYKPN QVDLFNTRAT KTQFESWYSA VKVEYDLNDE QMGVIMNGFM VWCIDNGTSP DVNGVWVMMD GEEQVEYPLK P IVENAKPT LRQIMHHFSD AAEAYIEMRN SESPYMPRYG LLRNLRDREL ARYAFDFYEV TSKTPNRARE AIAQMKAAAL AG INSRLFG LDGNISTNSE NTERHTARDV NQNMHTLLGM GPPQ UniProtKB: Coat protein |
-Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Macromolecule | Name: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 24 |
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Source (natural) | Organism: Watermelon mosaic virus |
Molecular weight | Theoretical: 1.485872 KDa |
Sequence | String: UUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 2-27 / Average electron dose: 1.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |