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- EMDB-54484: Echovirus 18 in situ, virion, C1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54484
TitleEchovirus 18 in situ, virion, C1
Map data
Sample
  • Virus: Echovirus E18
KeywordsVirus / in situ structure
Biological speciesEchovirus E18
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsMukhamedova L / Plevka P / Trebichalska Z / Novacek J
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Particles of echovirus 18 open to release their genomes in situ
Authors: Mukhamedova L / Plevka P / Trebichalska Z / Novacek J / Buchta D / Levdansky Y / Moravcova J / Hrebik D / Fuzik T / Tollefsrud TG / Andersen JT
History
DepositionJul 21, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54484.png

Downloads & links

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Map

FileDownload / File: emd_54484.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.08 Å/pix.
x 256 pix.
= 532.6 Å		2.08 Å/pix.
x 256 pix.
= 532.6 Å		2.08 Å/pix.
x 256 pix.
= 532.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.08047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.047296368 - 1.0078163
Average (Standard dev.)0.047919944 (±0.14445068)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 532.60034 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54484_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_54484_half_map_1.map
AnnotationHalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A

Fileemd_54484_half_map_2.map
AnnotationHalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Echovirus E18

EntireName: Echovirus E18
Components
  • Virus: Echovirus E18

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Supramolecule #1: Echovirus E18

SupramoleculeName: Echovirus E18 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 47506 / Sci species name: Echovirus E18 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.9 MDa
Virus shellShell ID: 1 / Diameter: 330.0 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1290 / Average exposure time: 8.0 sec. / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 42000
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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hbk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1337
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5
FSC plot (resolution estimation)

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