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- EMDB-24587: Cryo-EM reconstruction of Sulfolobus monocaudavirus SMV1, symmetry 3 -
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Open data
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Basic information
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Title | Cryo-EM reconstruction of Sulfolobus monocaudavirus SMV1, symmetry 3 | |||||||||
![]() | sym3 | |||||||||
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![]() | helical symmetry / archaeal virus / lemon-shaped virus / spindle-shaped virus / VIRUS | |||||||||
Function / homology | membrane / Hypothetical membrane protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
![]() | Wang F / Cvirkaite-Krupovic V | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome. Authors: Fengbin Wang / Virginija Cvirkaite-Krupovic / Matthijn Vos / Leticia C Beltran / Mark A B Kreutzberger / Jean-Marie Winter / Zhangli Su / Jun Liu / Stefan Schouten / Mart Krupovic / Edward H Egelman / ![]() ![]() ![]() Abstract: Spindle- or lemon-shaped viruses infect archaea in diverse environments. Due to the highly pleomorphic nature of these virions, which can be found with cylindrical tails emanating from the spindle- ...Spindle- or lemon-shaped viruses infect archaea in diverse environments. Due to the highly pleomorphic nature of these virions, which can be found with cylindrical tails emanating from the spindle-shaped body, structural studies of these capsids have been challenging. We have determined the atomic structure of the capsid of Sulfolobus monocaudavirus 1, a virus that infects hosts living in nearly boiling acid. A highly hydrophobic protein, likely integrated into the host membrane before the virions assemble, forms 7 strands that slide past each other in both the tails and the spindle body. We observe the discrete steps that occur as the tail tubes expand, and these are due to highly conserved quasiequivalent interactions with neighboring subunits maintained despite significant diameter changes. Our results show how helical assemblies can vary their diameters, becoming nearly spherical to package a larger genome and suggest how all spindle-shaped viruses have evolved from archaeal rod-like viruses. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 94.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.3 KB 9.3 KB | Display Display | ![]() |
Images | ![]() | 92.5 KB | ||
Filedesc metadata | ![]() | 4.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ro4MC ![]() 7ro2C ![]() 7ro3C ![]() 7ro5C ![]() 7ro6C ![]() 7robC ![]() 7rocC ![]() 7rodC ![]() 7roeC ![]() 7rogC ![]() 7rohC ![]() 7roiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | sym3 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Sulfolobus monocaudavirus SMV1
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Sulfolobus monocaudavirus SMV1
Supramolecule | Name: Sulfolobus monocaudavirus SMV1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1351702 / Sci species name: Sulfolobus monocaudavirus SMV1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: major capsid protein
Macromolecule | Name: major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.179297 KDa |
Sequence | String: MSVSVVVPSA KATGAGGKKA KTFKVIKVST PKVNNVHVPK IKKATRIHDP GAISGSLAKV TFGTNGFDIP TIAIALLIVG VIIGLSGLI LSIFATATAS AISNPSPGTL AYNLTHPLIN GMVSFFSFFP TLYVLLGVTG IVLIAAGIIS IIMEKFKT UniProtKB: Hypothetical membrane protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 6 |
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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 K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 0.7 Å Applied symmetry - Helical parameters - Δ&Phi: -155.5 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 59521 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |