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- EMDB-32709: EV71 VLP maps embedded in crystalline ice -

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Basic information

Entry
Database: EMDB / ID: EMD-32709
TitleEV71 VLP maps embedded in crystalline ice
Map dataThe EM map of EV71 VLP from crystal-embedded datasets frozen at -183 degree collected via Titan Krios by K2 camera
Sample
  • Virus: Enterovirus A71
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / host cell cytoplasm / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
Methodsingle particle reconstruction / Resolution: 3.2 Å
AuthorsZhang X / Shi H / Wu C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930069 China
CitationJournal: Structure / Year: 2023
Title: Addressing compressive deformation of proteins embedded in crystalline ice.
Authors: Huigang Shi / Chunling Wu / Xinzheng Zhang /
Abstract: For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. ...For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions.
History
DepositionJan 25, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32709.png

Downloads & links

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Map

FileDownload / File: emd_32709.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe EM map of EV71 VLP from crystal-embedded datasets frozen at -183 degree collected via Titan Krios by K2 camera
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 420 pix.
= 344.4 Å		0.82 Å/pix.
x 420 pix.
= 344.4 Å		0.82 Å/pix.
x 420 pix.
= 344.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.03322463 - 0.06996652
Average (Standard dev.)0.00044179638 (±0.005749098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32709_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: EV71 VLP map from crystal-embedded datasets frozen at...

Fileemd_32709_additional_1.map
AnnotationEV71 VLP map from crystal-embedded datasets frozen at -60 degree collected via Titan Kcrios by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: EV71 VLP map from crystal-embedded datasets frozen at...

Fileemd_32709_additional_2.map
AnnotationEV71 VLP map from crystal-embedded datasets frozen at -100 degree collected via Titan Kcrios by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: EV71 VLP map from crystal-embedded datasets frozen at...

Fileemd_32709_additional_3.map
AnnotationEV71 VLP map from crystal-embedded datasets frozen at -140 degree collected via FEI Arctica by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: EV71 VLP map from standard freezing datasets collected...

Fileemd_32709_additional_4.map
AnnotationEV71 VLP map from standard freezing datasets collected via Titan Krios by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of EV71 VLP from crystal-embedded...

Fileemd_32709_half_map_1.map
AnnotationThe half map of EV71 VLP from crystal-embedded datasets frozen at -183 degree collected via Titan Krios by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of EV71 VLP from crystal-embedded...

Fileemd_32709_half_map_2.map
AnnotationThe half map of EV71 VLP from crystal-embedded datasets frozen at -183 degree collected via Titan Krios by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Enterovirus A71

EntireName: Enterovirus A71
Components
  • Virus: Enterovirus A71

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Supramolecule #1: Enterovirus A71

SupramoleculeName: Enterovirus A71 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 39054 / Sci species name: Enterovirus A71 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROCOMPLEX / Virus enveloped: No / Virus empty: Yes

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Sugar embeddingMaterial: crystalline ice

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5219
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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