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- EMDB-18944: Structure of coxsackievirus B5 capsid (mutant CVB5F.cas.genogroup... -

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Basic information

Entry
Database: EMDB / ID: EMD-18944
TitleStructure of coxsackievirus B5 capsid (mutant CVB5F.cas.genogroupB) - E particle
Map dataMain map
Sample
  • Virus: Coxsackievirus B5
    • Protein or peptide: Genome polyprotein
KeywordsEnterovirus / coxsackievirus / thermostable / mutant / VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / 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 VP4 superfamily / 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 VP4 superfamily / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 B5
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsKumar K / Antanasijevic A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Environ Sci Technol / Year: 2024
Title: Influence of Amino Acid Substitutions in Capsid Proteins of Coxsackievirus B5 on Free Chlorine and Thermal Inactivation.
Authors: Shotaro Torii / Jérôme Gouttenoire / Kiruthika Kumar / Aleksandar Antanasijevic / Tamar Kohn /
Abstract: The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions ...The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions remains unknown. Here, we employed reverse genetics to investigate how amino acid substitutions in coxsackievirus B5 (CVB5) capsid proteins affect the virus' sensitivity to free chlorine and heat treatment. Of ten amino acid changes observed in CVB5 variants with free chlorine resistance, none significantly reduced the chlorine sensitivity, indicating a minor role of the capsid composition in chlorine sensitivity of CVB5. Conversely, a subset of these amino acid changes located at the C-terminal region of viral protein 1 led to reduced heat sensitivity. Cryo-electron microscopy revealed that these changes affect the assembly of intermediate viral states (altered and empty particles), suggesting that the mechanism for reduced heat sensitivity could be related to improved molecular packing of CVB5, resulting in greater stability or altered dynamics of virus uncoating during infection.
History
DepositionNov 19, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18944.png

Downloads & links

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Map

FileDownload / File: emd_18944.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Voxel sizeX=Y=Z: 0.926 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.15348025 - 0.43347406
Average (Standard dev.)0.0023537723 (±0.031110136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 444.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18944_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_18944_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_18944_half_map_2.map
Annotationhalf map 2
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 B5

EntireName: Coxsackievirus B5
Components
  • Virus: Coxsackievirus B5
    • Protein or peptide: Genome polyprotein

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Supramolecule #1: Coxsackievirus B5

SupramoleculeName: Coxsackievirus B5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Particle E state of the CVB5F.cas.genogroupB mutant.
NCBI-ID: 12074 / Sci species name: Coxsackievirus B5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Capsid VP1-3 / Diameter: 300.0 Å

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B5
Molecular weightTheoretical: 93.795359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGAQVSTQKT GAHETGLNAS GNSIIHYTNM NYYKDSASNS ANRQEFAQDP GKFTEPVKDI MIKSMPALNS PSAEECGYSD RVRSITLGN STITTQECAN VVVGYGTWPT YLRDEEATAE DQPTQPDVAT CRFYTLESVM WQQSSPGWWW KFPDALSNMG L FGQNMQYH ...String:
MGAQVSTQKT GAHETGLNAS GNSIIHYTNM NYYKDSASNS ANRQEFAQDP GKFTEPVKDI MIKSMPALNS PSAEECGYSD RVRSITLGN STITTQECAN VVVGYGTWPT YLRDEEATAE DQPTQPDVAT CRFYTLESVM WQQSSPGWWW KFPDALSNMG L FGQNMQYH YLGRAGYTLH VQCNASKFHQ GCLLVVCVPE AEMGCATIAN KPDQKSLSNG ETANVFDSQN TSGQTAVQAN VI NAGMGIG VGNLTIFPHQ WINLRTNNSA TIVMPYVNSV PMDNMFRHNN FTLMIIPFAP LSYSTGATTY VPITVTVAPM CAE YNGLRL AGRQGLPTML TPGSNQFLTS DDFQSPSAMP QFDVTPEMAI PGQVNNLMEI AEVDSVVPVN NTEGKVMSIE AYQI PVQSN STNGSQVFGF PLIPGASSVL NRTLLGEILN YYTHWSGSIK LTFMFCGSAM ATGKFLLAYS PPGAGAPTTR KEAML GTHV IWDVGLQSSC VLCIPWISQT HYRYVVMDEY TAGGYITCWY QTNIVVPADT QSDCKILCFV SACNDFSVRM LKDTPF IKQ DSFFQGPPGE AIERAIARVA DTISSGPVNS ESIPALTAAE TGHTSQVVPA DTMQTRHVKN YHSRSESTVE NFLCRSA CV YYTTYKNHGT DGDNFAQWVI NTRQVAQLRR KLEMFTYARF DLELTFVITS SQEQSTIKGQ DSPVLTHQIM YVPPGGPV P TKINSYSWQT STNPSVFWTE GSAPPRISIP FISIGNAYSM FYDGWARFDK QGTYGINTLN NMGTLYMRHV NDGSPGPIV STVRIYFKPK HVKTWVPRPP RLCQYQKAGN VNFEPSGVTE GRTEITAMQT T

UniProtKB: Genome polyprotein

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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

Concentration4.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMTris-HClTrisTris-HClTris
150.0 mMNaClSodium chlorideSodium chloride

Details: TBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
Details: 3ul of sample applied. Blotting time varied. Blotting force = 0. Total blots = 1..
DetailsInactivated by formaldehyde. Purified using a combination of sucrose gradient and size-exclusion chromatography.

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 6653 / Average electron dose: 40.0 e/Å2

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Image processing

Particle selectionNumber selected: 161820 / Details: Template picker used
Startup modelType of model: OTHER / Details: Ab initio model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 8 / Software - Name: cryoSPARC / Details: Heterogeneous refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Details: Non-uniform refinement. Icosahedral symmetry applied
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: Non-uniform refinement in cryoSPARC / Number images used: 75212
DetailsEER files were imported to cryoSPARC live and motion correction was performed with Patch.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7wl3


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: Asymmetric unit used for fitting and interpretation
DetailsInitial fitting was performed in Chimera and model refinement was performed in Coot and Rosetta.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8r5z:
Structure of coxsackievirus B5 capsid (mutant CVB5F.cas.genogroupB) - E particle

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