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- PDB-9y2z: Icosahedral symmetric structure of an expansion intermediate of T... -

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Basic information

Entry
Database: PDB / ID: 9y2z
TitleIcosahedral symmetric structure of an expansion intermediate of Turnip Crinkle Virus (Asymmetric Trimer Unit)
ComponentsCapsid protein
KeywordsVIRUS / Icosahedral non-enveloped ssRNA virus / Expansion intermediate
Function / homologyPlant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / symbiont-mediated suppression of host innate immune response / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Biological speciesTurnip crinkle virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsVenkatakrishnan, V. / Braet, S. / Ramesh, R. / Clawson, M.A. / Laremore, T.N. / Wong, S.M. / Anand, G.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM158169-01 United States
CitationJournal: To Be Published
Title: Novel asymmetric isopeptide bond steers directional genomic RNA egress from icosahedral virus
Authors: Venkatakrishnan, V. / Braet, S. / Ramesh, R. / Clawson, M.A. / Laremore, T.N. / Wong, S.M. / Anand, G.S.
History
DepositionSep 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,5133
Polymers114,5133
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)6,870,769180
Polymers6,870,769180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein / Coat protein / p38


Mass: 38170.941 Da / Num. of mol.: 3 / Fragment: R domain / Source method: isolated from a natural source / Details: TCV CP / Source: (natural) Turnip crinkle virus / References: UniProt: P06663
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: Turnip crinkle virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 8.2 MDa / Experimental value: NO
Source (natural)Organism: Turnip crinkle virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Brassica rapa subsp. rapa
Virus shellDiameter: 350 nm / Triangulation number (T number): 3
Buffer solutionpH: 5.4
Buffer componentConc.: 20 mM / Name: Sodium Acetate / Formula: CH3COONa
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 40000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 2036

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
4cryoSPARC4.2CTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
12cryoSPARC4.6classification
13cryoSPARC4.63D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60938 / Symmetry type: POINT
Atomic model buildingB value: 76 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 3ZX8

3zx8


Accession code: 3ZX8 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.87 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036357
ELECTRON MICROSCOPYf_angle_d0.7378647
ELECTRON MICROSCOPYf_dihedral_angle_d5.098896
ELECTRON MICROSCOPYf_chiral_restr0.053981
ELECTRON MICROSCOPYf_plane_restr0.0071130

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