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- PDB-7rod: Cryo-EM reconstruction of Sulfolobus monocaudavirus SMV1, symmetry 8 -

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Basic information

Entry
Database: PDB / ID: 7rod
TitleCryo-EM reconstruction of Sulfolobus monocaudavirus SMV1, symmetry 8
Componentsmajor capsid protein
KeywordsVIRUS / helical symmetry / archaeal virus / lemon-shaped virus / spindle-shaped virus
Function / homologymembrane / Hypothetical membrane protein
Function and homology information
Biological speciesSulfolobus monocaudavirus SMV1
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang, F. / Cvirkaite-Krupovic, V. / Krupovic, M. / Egelman, E.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: Cell / Year: 2022
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
DepositionJul 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: major capsid protein


Theoretical massNumber of molelcules
Total (without water)16,1791
Polymers16,1791
Non-polymers00
Water00
1
A: major capsid protein
x 203


Theoretical massNumber of molelcules
Total (without water)3,284,397203
Polymers3,284,397203
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation202
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 7 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 203 / Rise per n subunits: 4.378 Å / Rotation per n subunits: -7.716 °)

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Components

#1: Protein major capsid protein


Mass: 16179.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sulfolobus monocaudavirus SMV1 / References: UniProt: W0UUV5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Sulfolobus monocaudavirus SMV1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sulfolobus monocaudavirus SMV1
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -7.716 ° / Axial rise/subunit: 4.378 Å / Axial symmetry: C7
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 256976 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004147210
ELECTRON MICROSCOPYf_angle_d0.703201390
ELECTRON MICROSCOPYf_dihedral_angle_d4.15419950
ELECTRON MICROSCOPYf_chiral_restr0.04826460
ELECTRON MICROSCOPYf_plane_restr0.00724150

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