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- EMDB-11165: Coxsackievirus B4 in complex with capsid binder compound 48 -

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Basic information

Entry
Database: EMDB / ID: EMD-11165
TitleCoxsackievirus B4 in complex with capsid binder compound 48
Map data
SampleCoxsackievirus B4 (strain E2):
virus / (Genome polyprotein) x 4 / (ligand) x 2
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
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein like / Poliovirus 3A protein-like / Peptidase C3, picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus 2B protein / Picornavirus core protein 2A / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein (VP4) / Picornavirus coat protein VP4 ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein like / Poliovirus 3A protein-like / Peptidase C3, picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus 2B protein / Picornavirus core protein 2A / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein (VP4) / Picornavirus coat protein VP4 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / picornavirus capsid protein / Picornavirus capsid / 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 / 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 / Reverse transcriptase/Diguanylate cyclase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCoxsackievirus B4 (strain E2)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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.
History
DepositionJun 11, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 24, 2021-
Current statusMar 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00928
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00928
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zck
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zck
  • 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_11165.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 445.2 Å
1.06 Å/pix.
x 420 pix.
= 445.2 Å
1.06 Å/pix.
x 420 pix.
= 445.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.00928 / Movie #1: 0.00928
Minimum - Maximum-0.035159986 - 0.07784694
Average (Standard dev.)0.001138117 (±0.0055316053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 445.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z445.200445.200445.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0350.0780.001

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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)
Details: Virus harvested in BGM cells and purified in CsCl gradient.
Number of components: 7

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

VirusName: Coxsackievirus B4 (strain E2) / Class: VIRION
Details: Virus harvested in BGM cells and purified in CsCl gradient.
Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Coxsackievirus B4 (strain E2)
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: Icosahedron / 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: 6.434121 kDa
SourceSpecies: Coxsackievirus B4 (strain E2)

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Component #6: ligand, 2-oxidanyl-4-[(6-propoxynaphthalen-2-yl)sulfonylamino]ben...

LigandName: 2-oxidanyl-4-[(6-propoxynaphthalen-2-yl)sulfonylamino]benzoic acid
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.401433 kDa

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Component #7: ligand, MYRISTIC ACID

LigandName: MYRISTIC ACID / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.228371 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 47 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 13252
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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