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- EMDB-63430: Sub-atomic resolution structure of Native Flock House Virus with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63430
TitleSub-atomic resolution structure of Native Flock House Virus with applied icosahedral symmetry.
Map dataprimary map generated when the final refinement map(Map_sharp.mrc) was taken to phenix for autosharpening job.
Sample
  • Virus: Flock House virus
KeywordsIcosahedral Reconstruction / Non-Enveloped Virus / Flock House Virus / Single Particle Reconstruction / VIRUS
Biological speciesFlock House virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsSuhag K / Banerjee M
Funding support India, 1 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)EMR/2015/000644 India
CitationJournal: To Be Published
Title: Genome organization of a non-enveloped Icosahedral virus.
Authors: Suhag K / Banerjee M
History
DepositionFeb 13, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63430.png

Downloads & links

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Map

FileDownload / File: emd_63430.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map generated when the final refinement map(Map_sharp.mrc) was taken to phenix for autosharpening job.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-5.068024 - 15.692574499999999
Average (Standard dev.)0.000000000001869 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63430_msk_1.map
Projections & Slices
AxesZYX

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Additional map: This is the raw map generated during the final round of refinement.

Fileemd_63430_additional_1.map
AnnotationThis is the raw map generated during the final round of refinement.
Projections & Slices
AxesZYX

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Additional map: This is the final sharpened map generated during...

Fileemd_63430_additional_2.map
AnnotationThis is the final sharpened map generated during the final round of refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map2

Fileemd_63430_half_map_1.map
AnnotationHalf map2
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Half map1

Fileemd_63430_half_map_2.map
AnnotationHalf map1
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AxesZYX

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Slices (1/2)
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Sample components

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Entire : Flock House virus

EntireName: Flock House virus
Components
  • Virus: Flock House virus

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Supramolecule #1: Flock House virus

SupramoleculeName: Flock House virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: RNA1 and RNA2 of Flock House Virus (FHV) were co-transfected in Schneider's line 1 (DL1) cells for generation of FHV followed by purification using standard protocol.
NCBI-ID: 12287 / Sci species name: Flock House virus / Sci species strain: Flock House virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Drosophila (fruit flies)
Molecular weightTheoretical: 9 MDa
Virus shellShell ID: 1 / Diameter: 340.0 Å / T number (triangulation number): 3

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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

Concentration1 mg/mL
BufferpH: 7 / Component - Concentration: 50.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HEPES
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 292.15 K / Instrument: FEI VITROBOT MARK IV
Details: Use wait time of 12s and blot time of 3s before plunging in ethane..

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.15 K / Max: 77.15 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsAll alignment procedures were used.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 12617 / Average exposure time: 2.6 sec. / Average electron dose: 40.3 e/Å2 / Details: 38 frames/s, tiff gain corrected movies
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe movies were collected in tiff gain normalized format and imported to cryoSPARC for further reconstruction. The movies with a CTF fit resolution better than 7Angstrom and good relative ice thickness were taken forward.
Particle selectionNumber selected: 138720
Details: A few hundred micrographs were used to pick particles using blob picker and 2D classification was run. The best 2D classes were used for a template based particle picking on the complete data set.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.0) / Software - details: Patch CTF estimation was used / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 10 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 99474
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final 3D classificationNumber classes: 10 / Avg.num./class: 9947 / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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