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- EMDB-11300: Coxsackievirus B4 strain E2 -

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Basic information

Entry
Database: EMDB / ID: EMD-11300
TitleCoxsackievirus B4 strain E2
Map data
SampleCoxsackievirus B4 (strain E2):
virus / (Genome polyprotein) x 4
Function / homology
Function and homology information


suppression by virus of host RIG-I activity / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / integral to membrane of host cell / pore formation by virus in membrane of host cell ...suppression by virus of host RIG-I activity / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / integral to membrane of host cell / pore formation by virus in membrane of host cell / protein complex oligomerization / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / suppression by virus of host gene expression / ion channel activity / induction by virus of host autophagy / DNA replication / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / virion attachment to host cell / host cell nucleus / structural molecule activity / RNA binding / ATP binding / metal ion binding
RNA-directed RNA polymerase, catalytic domain / Picornavirus/Calicivirus coat protein / P-loop containing nucleoside triphosphate hydrolase / Peptidase C3, picornavirus core protein 2A / Peptidase S1, PA clan / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Viral coat protein subunit / Picornavirus capsid ...RNA-directed RNA polymerase, catalytic domain / Picornavirus/Calicivirus coat protein / P-loop containing nucleoside triphosphate hydrolase / Peptidase C3, picornavirus core protein 2A / Peptidase S1, PA clan / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Viral coat protein subunit / Picornavirus capsid / Picornavirus 2B protein / Poliovirus 3A protein-like / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Picornavirales 3C/3C-like protease domain / AAA+ ATPase domain / Helicase, superfamily 3, single-stranded RNA virus
Genome polyprotein
Biological speciesCoxsackievirus B4 (strain E2)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFlatt JW / Domanska A / Butcher SJ
Funding support Finland, 2 items
OrganizationGrant numberCountry
Academy of Finland315950 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Commun Biol / Year: 2021
Title: Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses.
Authors: Justin W Flatt / Aušra Domanska / Alma L Seppälä / Sarah J Butcher /
Abstract: Enteroviruses pose a persistent and widespread threat to human physical health, with no specific treatments available. Small molecule capsid binders have the potential to be developed as antivirals ...Enteroviruses pose a persistent and widespread threat to human physical health, with no specific treatments available. Small molecule capsid binders have the potential to be developed as antivirals that prevent virus attachment and entry into host cells. To aid with broad-range drug development, we report here structures of coxsackieviruses B3 and B4 bound to different interprotomer-targeting capsid binders using single-particle cryo-EM. The EM density maps are beyond 3 Å resolution, providing detailed information about interactions in the ligand-binding pocket. Comparative analysis revealed the residues that form a conserved virion-stabilizing network at the interprotomer site, and showed the small molecule properties that allow anchoring in the pocket to inhibit virus disassembly.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 3, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00816
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00816
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zms
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zms
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11300.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 400 pix.
= 496. Å
1.24 Å/pix.
x 400 pix.
= 496. Å
1.24 Å/pix.
x 400 pix.
= 496. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 0.00816 / Movie #1: 0.00816
Minimum - Maximum-0.04550528 - 0.083117016
Average (Standard dev.)0.0009391678 (±0.0053684674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 496.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z496.000496.000496.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0460.0830.001

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Supplemental data

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Sample components

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Entire Coxsackievirus B4 (strain E2)

EntireName: Coxsackievirus B4 (strain E2) / Number of components: 5

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Component #1: virus, Coxsackievirus B4 (strain E2)

VirusName: Coxsackievirus B4 (strain E2) / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Coxsackievirus B4 (strain E2)
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: icosahedral / Diameter: 300.0 Å / T number (triangulation number): 3

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Component #2: protein, Genome polyprotein

ProteinName: Genome polyprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.685498 kDa
SourceSpecies: Coxsackievirus B4 (strain E2)

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Component #3: protein, Genome polyprotein

ProteinName: Genome polyprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.70807 kDa
SourceSpecies: Coxsackievirus B4 (strain E2)

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Component #4: protein, Genome polyprotein

ProteinName: Genome polyprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.44416 kDa
SourceSpecies: Coxsackievirus B4 (strain E2)

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Component #5: protein, Genome polyprotein

ProteinName: Genome polyprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.499235 kDa
SourceSpecies: Coxsackievirus B4 (strain E2)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: TFS TALOS F200C
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 40627
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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