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- EMDB-32611: Structure of Coxsackievirus A10 with Hybrid electron counting at ... -

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Basic information

Entry
Database: EMDB / ID: EMD-32611
TitleStructure of Coxsackievirus A10 with Hybrid electron counting at 200 kV
Map dataCoxsackievirus A10 Hybrid at 200 kV
Sample
  • Virus: Coxsackievirus A10
KeywordsCoxsackievirus A10 / VIRUS
Biological speciesCoxsackievirus A10
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsZhu DJ / Zhang XZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930069 China
CitationJournal: Commun Biol / Year: 2022
Title: An electron counting algorithm improves imaging of proteins with low-acceleration-voltage cryo-electron microscope.
Authors: Dongjie Zhu / Huigang Shi / Chunling Wu / Xinzheng Zhang /
Abstract: Relative to the 300-kV accelerating field, electrons accelerated under lower voltages are potentially scattered more strongly. Lowering the accelerate voltage has been suggested to enhance the signal- ...Relative to the 300-kV accelerating field, electrons accelerated under lower voltages are potentially scattered more strongly. Lowering the accelerate voltage has been suggested to enhance the signal-to-noise ratio (SNR) of cryo-electron microscopy (cryo-EM) images of small-molecular-weight proteins (<100 kD). However, the detection efficient of current Direct Detection Devices (DDDs) and temporal coherence of cryo-EM decrease at lower voltage, leading to loss of SNR. Here, we present an electron counting algorithm to improve the detection of low-energy electrons. The counting algorithm increased the SNR of 120-kV and 200-kV cryo-EM image from a Falcon III camera by 8%, 20% at half the Nyquist frequency and 21%, 80% at Nyquist frequency, respectively, resulting in a considerable improvement in resolution of 3D reconstructions. Our results indicate that with further improved temporal coherence and a dedicated designed camera, a 120-kV cryo-electron microscope has potential to match the 300-kV microscope at imaging small proteins.
History
DepositionJan 15, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32611.png

Downloads & links

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Map

FileDownload / File: emd_32611.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCoxsackievirus A10 Hybrid at 200 kV
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.0104
Minimum - Maximum-0.023990812 - 0.036996324
Average (Standard dev.)0.00000002526708 (±0.0020429248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32611_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half2

Fileemd_32611_half_map_1.map
AnnotationHalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half1

Fileemd_32611_half_map_2.map
AnnotationHalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Coxsackievirus A10

EntireName: Coxsackievirus A10
Components
  • Virus: Coxsackievirus A10

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Supramolecule #1: Coxsackievirus A10

SupramoleculeName: Coxsackievirus A10 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 42769 / Sci species name: Coxsackievirus A10 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 10.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

30254

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 11048
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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