+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9204 | |||||||||
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Title | Cucumber Leaf Spot Virus | |||||||||
Map data | Cucumber leaf spot virus | |||||||||
Sample |
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Keywords | Plant virus / Tombusvirus / CLSV / VIRUS | |||||||||
Function / homology | Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / Capsid protein Function and homology information | |||||||||
Biological species | Cucumber leaf spot virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Sherman MB / Smith TJ | |||||||||
Citation | Journal: J Virol / Year: 2020 Title: Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes. Authors: Michael B Sherman / Richard Guenther / Ron Reade / D'Ann Rochon / Tim Sit / Thomas J Smith / Abstract: Members of the family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the family have single-stranded ...Members of the family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the family have single-stranded RNA (ssRNA) genomes with T=3 icosahedral protein shells with a maximum diameter of ∼340 Å. Each capsid protein is comprised of three domains: R (RNA binding), S (shell), and P (protruding). Between the R domain and S domain is the "arm" region that studies have shown to play a critical role in assembly. To better understand how the details of structural differences and similarities influence the viral life cycles, the structures of cucumber leaf spot virus (CLSV; genus ) and red clover necrotic mosaic virus (RCNMV; genus ) were determined to resolutions of 3.2 Å and 2.9 Å, respectively, with cryo-electron microscopy and image reconstruction methods. While the shell domains had homologous structures, the stabilizing interactions at the icosahedral 3-fold axes and the R domains differed greatly. The heterogeneity in the R domains among the members of the family is likely correlated with differences in the sizes and characteristics of the corresponding genomes. We propose that the changes in the R domain/RNA interactions evolved different arm domain interactions at the β-annuli. For example, RCNMV has the largest genome and it appears to have created the necessary space in the capsid by evolving the shortest R domain. The resulting loss in RNA/R domain interactions may have been compensated for by increased intersubunit β-strand interactions at the icosahedral 3-fold axes. Therefore, the R and arm domains may have coevolved to package different genomes within the conserved and rigid shell. Members of the family have nearly identical shells, and yet they package genomes that range from 4.6 kb (monopartite) to 5.3 kb (bipartite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high-resolution cryo-electron microscopy (cryo-EM) structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the "arm," seems to have also coevolved with the R domain to allow particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle. | |||||||||
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_9204.map.gz | 141.7 MB | EMDB map data format | |
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Header (meta data) | emd-9204-v30.xml emd-9204.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_9204.png | 262.8 KB | ||
Filedesc metadata | emd-9204.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9204 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9204 | HTTPS FTP |
-Validation report
Summary document | emd_9204_validation.pdf.gz | 599.7 KB | Display | EMDB validaton report |
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Full document | emd_9204_full_validation.pdf.gz | 599.3 KB | Display | |
Data in XML | emd_9204_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | emd_9204_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9204 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9204 | HTTPS FTP |
-Related structure data
Related structure data | 6mrlMC 9205C 6mrmC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9204.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cucumber leaf spot virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.845 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 : Cucumber leaf spot virus
Entire | Name: Cucumber leaf spot virus |
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Components |
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-Supramolecule #1: Cucumber leaf spot virus
Supramolecule | Name: Cucumber leaf spot virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 165432 / Sci species name: Cucumber leaf spot virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: p41
Macromolecule | Name: p41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Cucumber leaf spot virus |
Molecular weight | Theoretical: 41.151074 KDa |
Sequence | String: MEIARTNKNS VVKYVPAAVG AAYQMGKSIV PYAPTIVDAL GNVVSRATGR KKKSKGKEVQ NQIVGGIGAI AAPVSITKRV RGMRPSFRQ TKGKVHIVHR ELVTSVINLV GNFRVNNNVS AQIGQFRINP SNSSLFTWLP TIASNFDSYR FTSIRFVYVP L CATTETGR ...String: MEIARTNKNS VVKYVPAAVG AAYQMGKSIV PYAPTIVDAL GNVVSRATGR KKKSKGKEVQ NQIVGGIGAI AAPVSITKRV RGMRPSFRQ TKGKVHIVHR ELVTSVINLV GNFRVNNNVS AQIGQFRINP SNSSLFTWLP TIASNFDSYR FTSIRFVYVP L CATTETGR VSLFWDKDSQ DPLPVDRAAL SSYGHSNEGP PWAETTLNVP TDGKQRFVTD SNTTDRKLVD LGQFAFATYA GG SNNQIGD IYVEYGVEFS EAQPAGGLTQ YITKSVGATA STTGPSYVVD ANINVNATTA NVEFFSPGTF LITAVVYGST IAS PSMAGG NGTLIGDLPV VGGSNASIWT CVFSTTGVST SVPTFTQAGT GLTRVQYTIT RVNSQTAYQV UniProtKB: Capsid protein |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 6 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL 3000SFF |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1246 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |