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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: Sci Adv / Year: 2025
Title: Asymmetric isopeptide bond steers directional genomic RNA egress from icosahedral virus.
Authors: Sean M Braet / Varun Venkatakrishnan / Ranita Ramesh / Molly A Clawson / Tatiana N Laremore / Sek-Man Wong / Ganesh S Anand /
Abstract: Icosahedral RNA viruses rely upon essential asymmetries for directional genome egress into the host cell. How these asymmetric egress points are built into the quaternary assembly of the virion is ...Icosahedral RNA viruses rely upon essential asymmetries for directional genome egress into the host cell. How these asymmetric egress points are built into the quaternary assembly of the virion is unknown. Here, we capture the structure and dynamics of a partially expanded virus disassembly intermediate, poised to release its spring-loaded genomic RNA. The structure shows highly localized density of RNA underneath surface fivefold axes on one-half of the viral particle. This polarity in RNA distribution is associated with a unique interchain isopeptide bond (glutamic acid-lysine), which flanks conserved high-affinity RNA binding sites. This singular isopeptide bond at the asymmetric egress site confers an essential "loaded-die" feature that is critical for steering genomic RNA egress into the host cell for virus propagation.
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
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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)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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