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- EMDB-24606: EV-71 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-24606
TitleEV-71
Map dataEV71
Sample
  • Virus: Eastern equine encephalitis virus
KeywordsEnterovirus / EV71 / VIRUS
Biological speciesEastern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen C-L / Kuhn RJ / Klose T
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095366 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI142790 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095436 United States
Defense Threat Reduction Agency (DTRA)HDTRA1-15-1-0047 United States
Defense Threat Reduction Agency (DTRA)HDTRA1-15-1-0013 United States
CitationJournal: Not published
Title: EV-71
Authors: Chen C-L / Kuhn RJ / Klose T
History
DepositionAug 2, 2021-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24606.png

Downloads & links

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Map

FileDownload / File: emd_24606.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEV71
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 384 pix.
= 622.08 Å		1.62 Å/pix.
x 384 pix.
= 622.08 Å		1.62 Å/pix.
x 384 pix.
= 622.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0
Minimum - Maximum-36.315975000000002 - 59.826549999999997
Average (Standard dev.)0.0214887 (±2.5363932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 622.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Eastern equine encephalitis virus

EntireName: Eastern equine encephalitis virus
Components
  • Virus: Eastern equine encephalitis virus

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Supramolecule #1: Eastern equine encephalitis virus

SupramoleculeName: Eastern equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Equus caballus (horse)
Virus shellShell ID: 1 / Diameter: 660.0 Å

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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

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris
0.1 mMNa2HPO4sodium phosphate dibasic
EDTA

Details: pH 8
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 / Details: blot for 3.3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 100.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 38000
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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 2344
Initial angle assignmentType: COMMON LINE / Software - Name: jspr (ver. 2017)
Final angle assignmentType: COMMON LINE / Software - Name: jspr (ver. 2017)
FSC plot (resolution estimation)

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