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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10129 | |||||||||
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Title | Cryo-EM structure of TMV in water | |||||||||
![]() | B-factor sharpened and locally filtered | |||||||||
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Function / homology | Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / identical protein binding / Capsid protein![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 1.9 Å | |||||||||
![]() | Weis F / Beckers M / Sachse C | |||||||||
![]() | ![]() Title: Elucidation of the viral disassembly switch of tobacco mosaic virus. Authors: Felix Weis / Maximilian Beckers / Iris von der Hocht / Carsten Sachse / ![]() Abstract: Stable capsid structures of viruses protect viral RNA while they also require controlled disassembly for releasing the viral genome in the host cell. A detailed understanding of viral disassembly ...Stable capsid structures of viruses protect viral RNA while they also require controlled disassembly for releasing the viral genome in the host cell. A detailed understanding of viral disassembly processes and the involved structural switches is still lacking. This process has been extensively studied using tobacco mosaic virus (TMV), and carboxylate interactions are assumed to play a critical part in this process. Here, we present two cryo-EM structures of the helical TMV assembly at 2.0 and 1.9 Å resolution in conditions of high Ca concentration at low pH and in water. Based on our atomic models, we identify the conformational details of the disassembly switch mechanism: In high Ca /acidic pH environment, the virion is stabilized between neighboring subunits through carboxyl groups E95 and E97 in close proximity to a Ca binding site that is shared between two subunits. Upon increase in pH and lower Ca levels, mutual repulsion of the E95/E97 pair and Ca removal destabilize the network of interactions between adjacent subunits at lower radius and release the switch for viral disassembly. | |||||||||
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 | ![]() | 395 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.4 KB 20.4 KB | Display Display | ![]() |
Images | ![]() | 322.7 KB | ||
Masks | ![]() | 437.9 MB | ![]() | |
Others | ![]() ![]() ![]() | 16.4 MB 351 MB 351 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6saeMC ![]() 6sagC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Raw movies of the TMV in water sample, with corresponding start-end coordinates files and gain reference file [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | B-factor sharpened and locally filtered | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.638 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Confidence map
File | emd_10129_additional.map | ||||||||||||
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Annotation | Confidence map | ||||||||||||
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Density Histograms |
-Half map: Halfmap 1
File | emd_10129_half_map_1.map | ||||||||||||
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Annotation | Halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Halfmap 2
File | emd_10129_half_map_2.map | ||||||||||||
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Annotation | Halfmap 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Tobacco mosaic virus (strain vulgare)
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Tobacco mosaic virus (strain vulgare)
Supramolecule | Name: Tobacco mosaic virus (strain vulgare) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 12243 / Sci species name: Tobacco mosaic virus (strain vulgare) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 Details: Residues 154-158 are flexible and were not modelled. Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.531463 KDa |
Sequence | String: (ACE)SYSITTPSQ FVFLSSAWAD PIELINLCTN ALGNQFQTQQ ARTVVQRQFS EVWKPSPQVT VRFPDSDFKV YRYNAV LDP LVTALLGAFD TRNRIIEVEN QANPTTAETL DATRRVDDAT VAIRSAINNL IVELIRGTGS YNRSSFESSS GLVWTSG PA T |
-Macromolecule #2: RNA (5'-R(P*GP*AP*A)-3')
Macromolecule | Name: RNA (5'-R(P*GP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 958.66 Da |
Sequence | String: GAA |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 92 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Concentration | 22 mg/mL |
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Buffer | pH: 7 / Details: pure water |
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Details: Pelco Easyglow, factory settings |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-20 / Number grids imaged: 1 / Number real images: 62 / Average exposure time: 5.0 sec. / Average electron dose: 30.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.35 µm / Nominal defocus min: 0.15 µm / Nominal magnification: 215000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |