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- EMDB-72430: Symmetry relaxed asymmetric structure of an expansion intermediat... -

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Basic information

Entry
Database: EMDB / ID: EMD-72430
TitleSymmetry relaxed asymmetric structure of an expansion intermediate of Turnip crinkle virus
Map dataSymmetry relaxed (asymmetric) structure of Turnip Crinkle Virus expansion intermediate.
Sample
  • Virus: Turnip crinkle virus
    • Protein or peptide: Capsid protein
KeywordsIcosahedral non-enveloped ssRNA virus / Expansion intermediate / VIRAL PROTEIN
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: 3.62 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: To Be Published
Title: Novel asymmetric isopeptide bond steers directional genomic RNA egress from icosahedral virus
Authors: Venkatakrishnan V / Braet S / Ramesh R / Clawson MA / Laremore TN / Wong SM / Anand GS
History
DepositionSep 1, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72430.png

Downloads & links

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Map

FileDownload / File: emd_72430.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetry relaxed (asymmetric) structure of Turnip Crinkle Virus expansion intermediate.
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: 0.45
Minimum - Maximum-1.6867924 - 3.4331677
Average (Standard dev.)-0.0047231116 (±0.17694943)
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: Half-map of Symmetry relaxed (asymmetric) structure of Turnip...

Fileemd_72430_half_map_1.map
AnnotationHalf-map of Symmetry relaxed (asymmetric) structure of Turnip Crinkle Virus expansion intermediate.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of Symmetry relaxed (asymmetric) structure of Turnip...

Fileemd_72430_half_map_2.map
AnnotationHalf-map of Symmetry relaxed (asymmetric) structure of Turnip Crinkle Virus expansion intermediate.
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 / 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
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.62 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:

9y2z


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

PDB-9y31:
Symmetry relaxed asymmetric structure of an expansion intermediate of Turnip crinkle virus

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