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- EMDB-28627: Cryo-EM structure of Coxsackievirus A10 (empty) embedded in cryst... -

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Basic information

Entry
Database: EMDB / ID: EMD-28627
TitleCryo-EM structure of Coxsackievirus A10 (empty) embedded in crystalline ice
Map dataThe EM map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -140 celsius degree. The resolution of EM map is 3.1 angstrom.
Sample
  • Virus: Coxsackievirus A10
KeywordsCoxsackie A10 VLP / Crystalline ice / Crystal ice / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCoxsackievirus A10
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsShi H / Wu C / Zhang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)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
DepositionOct 20, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28627.png

Downloads & links

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Map

FileDownload / File: emd_28627.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe EM map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -140 celsius degree. The resolution of EM map is 3.1 angstrom.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 432 pix.
= 361.152 Å		0.84 Å/pix.
x 432 pix.
= 361.152 Å		0.84 Å/pix.
x 432 pix.
= 361.152 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.04077744 - 0.07279287
Average (Standard dev.)0.0007444865 (±0.00571324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 361.152 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28627_msk_1.map
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Additional map: The half map of Coxsackie A10 virus like...

Fileemd_28627_additional_1.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -183 celsius degree.
Projections & Slices
AxesZYX

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Additional map: The half map of Coxsackie A10 virus like...

Fileemd_28627_additional_10.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -100 celsius degree.
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Additional map: The half map of Coxsackie A10 virus like...

Fileemd_28627_additional_11.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -60 celsius degree.
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Additional map: The half map of Coxsackie A10 virus like...

Fileemd_28627_additional_12.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -60 celsius degree.
Projections & Slices
AxesZYX

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Additional map: The EM map of Coxsackie A10 virus like...

Fileemd_28627_additional_2.map
AnnotationThe EM map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -183 celsius degree. The resolution of EM map is 4.1 angstrom.
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AxesZYX

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Additional map: The half map of Coxsackie A10 virus like...

Fileemd_28627_additional_3.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -183 celsius degree.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Additional map: The EM map of Coxsackie A10 virus like...

Fileemd_28627_additional_4.map
AnnotationThe EM map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -100 celsius degree. The resolution of EM map is 3.9 angstrom.
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Additional map: The EM map of Coxsackie A10 virus like...

Fileemd_28627_additional_5.map
AnnotationThe EM map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -60 celsius degree. The resolution of EM map is 4.2 angstrom.
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AxesZYX

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Additional map: The half map of Coxsackie A10 virus like...

Fileemd_28627_additional_6.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in crystalline ice frozen at -100 celsius degree.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The EM map of Coxsackie A10 virus like...

Fileemd_28627_additional_7.map
AnnotationThe EM map of Coxsackie A10 virus like particle (empty) embedded in vitreous ice frozen at -183 celsius degree using standard procedure. The resolution of EM map is 4.0 angstrom.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Additional map: The half map of Coxsackie A10 virus like...

Fileemd_28627_additional_8.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in vitreous ice frozen at -183 celsius degree using standard procedure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The half map of Coxsackie A10 virus like...

Fileemd_28627_additional_9.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in vitreous ice frozen at -183 celsius degree using standard procedure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of Coxsackie A10 virus like...

Fileemd_28627_half_map_1.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in vitreous ice frozen at -183 celsius degree using standard procedure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of Coxsackie A10 virus like...

Fileemd_28627_half_map_2.map
AnnotationThe half map of Coxsackie A10 virus like particle (empty) embedded in vitreous ice frozen at -183 celsius degree using standard procedure.
Projections & Slices
AxesZYX

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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: VIRUS-LIKE PARTICLE / Virus isolate: SUBSPECIES / Virus enveloped: No / Virus empty: Yes

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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: 6.8 / Details: PBS, Ph 6.8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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 / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
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: INSILICO MODEL
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7945
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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