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- PDB-8vg6: Structure of Tulane virus -

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Basic information

Entry
Database: PDB / ID: 8vg6
TitleStructure of Tulane virus
ComponentsCapsid protein
KeywordsVIRUS / Tualne virus / Calicivirus / norovirus
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Viral coat protein subunit / host cell cytoplasm / Capsid protein
Function and homology information
Biological speciesTulane virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsYu, G. / Li, K. / Jiang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI111095 United States
CitationJournal: To Be Published
Title: Structure of Tulane virus
Authors: Yu, G. / Li, K. / Jiang, W.
History
DepositionDec 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Data collection / Category: em_software / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)173,6703
Polymers173,6703
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,420,210180
Polymers10,420,210180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 5


  • icosahedral pentamer
  • 868 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)868,35115
Polymers868,35115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.04 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,042,02118
Polymers1,042,02118
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein


Mass: 57890.055 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tulane virus / Plasmid: pBR322 / Cell line (production host): monkey kidney cells / Production host: Platyrrhini (New World monkeys) / References: UniProt: B2Y6D0
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tulane virus / Type: VIRUS / Details: Purified from cell cultures / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 10 MDa / Experimental value: NO
Source (natural)Organism: Tulane virus
Source (recombinant)Organism: Platyrrhini (New World monkeys) / Cell: Monkey kidney cells / Plasmid: pBR322
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Macaca
Virus shellDiameter: 400 nm
Buffer solutionpH: 7.4
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 / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412073
ELECTRON MICROSCOPYf_angle_d0.57816569
ELECTRON MICROSCOPYf_dihedral_angle_d4.8461644
ELECTRON MICROSCOPYf_chiral_restr0.0481861
ELECTRON MICROSCOPYf_plane_restr0.0042155

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