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- EMDB-72428: Icosahedral symmetric structure of an expansion intermediate of T... -

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Basic information

Entry
Database: EMDB / ID: EMD-72428
TitleIcosahedral symmetric structure of an expansion intermediate of Turnip Crinkle Virus (Asymmetric Trimer Unit)
Map dataIcosahedral symmetry averaged structure of an expansion intermediate of Turnip Crinkle Virus
Sample
  • Virus: Turnip crinkle virus
    • Protein or peptide: Capsid protein
KeywordsIcosahedral non-enveloped ssRNA virus / Expansion intermediate / VIRUS
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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsVenkatakrishnan V / Braet S / Ramesh R / Clawson MA / Laremore TN / Wong SM / Anand GS
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72428.png

Downloads & links

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Map

FileDownload / File: emd_72428.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral symmetry averaged structure of an expansion intermediate of Turnip Crinkle Virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 600 pix.
= 638.64 Å		1.06 Å/pix.
x 600 pix.
= 638.64 Å		1.06 Å/pix.
x 600 pix.
= 638.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0644 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-2.3881242 - 5.4332223
Average (Standard dev.)-0.0052448637 (±0.20883113)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 638.63995 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Icosahedral symmetry averaged hap map of an expansion...

Fileemd_72428_half_map_1.map
AnnotationIcosahedral symmetry averaged hap map of an expansion intermediate of Turnip Crinkle Virus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Icosahedral symmetry averaged hap map of an expansion...

Fileemd_72428_half_map_2.map
AnnotationIcosahedral symmetry averaged hap map of an expansion intermediate of Turnip Crinkle Virus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Turnip crinkle virus

EntireName: Turnip crinkle virus
Components
  • Virus: Turnip crinkle virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Turnip crinkle virus

SupramoleculeName: Turnip crinkle virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11988 / Sci species name: Turnip crinkle virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Brassica rapa subsp. rapa (turnip)
Molecular weightTheoretical: 8.2 MDa
Virus shellShell ID: 1 / Diameter: 350.0 Å / T number (triangulation number): 3

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Details: TCV CP / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Turnip crinkle virus
Molecular weightTheoretical: 38.170941 KDa
SequenceString: MENDPRVRKF ASDGAQWAIK WQKKGWSTLT SRQKQTARAA MGIKLSPVAQ PVQKVTRLSA PVALAYREVS TQPRVSTARD GITRSGSEL ITTLKKNTDT EPKYTTAVLN PSEPGTFNQL IKEAAQYEKY RFTSLRFRYS PMSPSTTGGK VALAFDRDAA K PPPNDLAS ...String:
MENDPRVRKF ASDGAQWAIK WQKKGWSTLT SRQKQTARAA MGIKLSPVAQ PVQKVTRLSA PVALAYREVS TQPRVSTARD GITRSGSEL ITTLKKNTDT EPKYTTAVLN PSEPGTFNQL IKEAAQYEKY RFTSLRFRYS PMSPSTTGGK VALAFDRDAA K PPPNDLAS LYNIEGCVSS VPWTGFILTV PTDSTDRFVA DGISDPKLVD FGKLIMATYG QGANDAAQLG EVRVEYTVQL KN RTGSTSD AQIGDFAGVK DGPRLVSWSK TKGTAGWEHD CHFLGTGNFS LTLFYEKAPV SGLENADASD FSVLGEAAAG SVQ WAGVKV AERGQGVKMV TTEEQPKGKW QALRI

UniProtKB: Capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 5.4 / Component - Concentration: 20.0 mM / Component - Formula: CH3COONa / Component - Name: Sodium Acetate
GridModel: Quantifoil R2/2 / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number real images: 2036 / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 40.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 60938
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 14 / Software - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3zx8


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 76
Output model

PDB-9y2z:
Icosahedral symmetric structure of an expansion intermediate of Turnip Crinkle Virus (Asymmetric Trimer Unit)

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