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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10373 | |||||||||
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Title | CryoEM structure for Turnip mosaic virus (TuMV) | |||||||||
![]() | CryoEM map for Turnip mosaic virus (TuMV) | |||||||||
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![]() | potyvirus / virion / helical virus / VIRUS | |||||||||
Function / homology | Potyvirus coat protein / Potyvirus coat protein / viral capsid / Coat protein / Coat protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 5.2 Å | |||||||||
![]() | Valle MV / Cuesta R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Turnip mosaic virus and its viral-like particles. Authors: Rebeca Cuesta / Carmen Yuste-Calvo / David Gil-Cartón / Flora Sánchez / Fernando Ponz / Mikel Valle / ![]() Abstract: Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide ...Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide representative of the Potyvirus genus, one of most abundant groups of plant viruses, which displays a very wide host range. We have studied by cryoEM the structure of TuMV virions and its viral-like particles (VLPs) to explore the role of the interactions between proteins and RNA in the assembly of the virions. The results show that the CP-RNA interaction is needed for the correct orientation of the CP N-terminal arm, a region that plays as a molecular staple between CP subunits in the fully assembled virion. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 19.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.3 KB 12.3 KB | Display Display | ![]() |
Images | ![]() | 197.4 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t34MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map for Turnip mosaic virus (TuMV) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : Turnip mosaic virus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Turnip mosaic virus
Supramolecule | Name: Turnip mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12230 / Sci species name: Turnip mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Coat protein
Macromolecule | Name: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.073395 KDa |
Sequence | String: PRLKSLTSKM RVPRYEKRVA LNLDHLILYT PEQTDLSNTR STRKQFDTWF EGVMADYELT EDKMQIILNG LMVWCIENGT SPNINGMWV MMDGDDQVEF PIKPLIDHAK PTFRQIMAHF SDVAEAYIEK RNQDRPYMPR YGLQRNLTDM SLARYAFDFY E MTSRTPIR ...String: PRLKSLTSKM RVPRYEKRVA LNLDHLILYT PEQTDLSNTR STRKQFDTWF EGVMADYELT EDKMQIILNG LMVWCIENGT SPNINGMWV MMDGDDQVEF PIKPLIDHAK PTFRQIMAHF SDVAEAYIEK RNQDRPYMPR YGLQRNLTDM SLARYAFDFY E MTSRTPIR AREAHIQMKA AALRGANNNL FGLDGNVGTT VENTERHTT 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 / Details: Model of ssRNA as polyU / Number of copies: 19 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.485872 KDa |
Sequence | String: UUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-31 / Number grids imaged: 1 / Average exposure time: 9.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.0 Å Applied symmetry - Helical parameters - Δ&Phi: -40.8 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 194432 |
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Segment selection | Number selected: 444678 / Software - Name: RELION (ver. 2) |
Startup model | Type of model: INSILICO MODEL In silico model: Cylinder with the diameter of the filament. |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 2) |