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- EMDB-7905: Structure of the EVA71 strain 11316 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-7905
TitleStructure of the EVA71 strain 11316 capsid
Map data
SampleEnterovirus A71:
virus / VP1 / VP2 / VP3 / VP4 / ligand
Function / homology
Function and homology information


picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell ...picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / viral capsid / RNA-directed RNA polymerase / suppression by virus of host gene expression / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
Peptidase C3A/C3B, picornaviral / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain ...Peptidase C3A/C3B, picornaviral / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3, picornavirus core protein 2A / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / P-loop containing nucleoside triphosphate hydrolase / Poliovirus core protein 3a, soluble domain / 3C cysteine protease (picornain 3C) / RNA dependent RNA polymerase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Picornavirus 2B protein / Picornavirus core protein 2A / RNA helicase / Poliovirus 3A protein-like
Genome polyprotein / Polyprotein / Genome polyprotein / Polyprotein
SourceEnterovirus A71
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSun L / Lee H / Thibaut HJ / Rivero-Buceta E / Martinez-Gualda B / Delang L / Leyssen P / Gago F / San-Felix A / Hafenstein S / Mirabelli C / Neyts J
CitationJournal: PLoS Pathog. / Year: 2019
Title: Viral engagement with host (co-)receptors blocked by a novel class of tryptophan dendrimers that targets the 5-fold-axis of the enterovirus-A71 capsid.
Authors: Liang Sun / Hyunwook Lee / Hendrik Jan Thibaut / Kristina Lanko / Eva Rivero-Buceta / Carol Bator / Belen Martinez-Gualda / Kai Dallmeier / Leen Delang / Pieter Leyssen / Federico Gago / Ana San-Félix / Susan Hafenstein / Carmen Mirabelli / Johan Neyts /
Abstract: Enterovirus A71 (EV-A71) is a non-polio neurotropic enterovirus with pandemic potential. There are no antiviral agents approved to prevent or treat EV-A71 infections. We here report on the molecular ...Enterovirus A71 (EV-A71) is a non-polio neurotropic enterovirus with pandemic potential. There are no antiviral agents approved to prevent or treat EV-A71 infections. We here report on the molecular mechanism by which a novel class of tryptophan dendrimers inhibits (at low nanomolar to high picomolar concentration) EV-A71 replication in vitro. A lead compound in the series (MADAL385) prevents binding and internalization of the virus but does not, unlike classical capsid binders, stabilize the particle. By means of resistance selection, reverse genetics and cryo-EM, we map the binding region of MADAL385 to the 5-fold vertex of the viral capsid and demonstrate that a single molecule binds to each vertex. By interacting with this region, MADAL385 prevents the interaction of the virus with its cellular (co-)receptors PSGL1 and heparan sulfate, thereby blocking the attachment of EV-A71 to the host cells.
Validation ReportPDB-ID: 6dij

SummaryFull reportAbout validation report
DateDeposition: May 23, 2018 / Header (metadata) release: Jun 13, 2018 / Map release: May 1, 2019 / Update: May 22, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6dij
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6dij
  • 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_7905.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 340 pix.
= 374. Å
1.1 Å/pix.
x 340 pix.
= 374. Å
1.1 Å/pix.
x 340 pix.
= 374. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.15266198 - 0.23023732
Average (Standard dev.)0.0024396195 (±0.015669325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-170-170-170
Dimensions340340340
Spacing340340340
CellA=B=C: 374.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z374.000374.000374.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-170-170-170
NC/NR/NS340340340
D min/max/mean-0.1530.2300.002

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Supplemental data

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Sample components

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Entire Enterovirus A71

EntireName: Enterovirus A71 / Number of components: 6

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Component #1: virus, Enterovirus A71

VirusName: Enterovirus A71Enterovirus 71 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Enterovirus A71

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Component #2: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.748754 kDa
SourceSpecies: Enterovirus A71 / Strain: B2-11316-86

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Component #3: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.946342 kDa
SourceSpecies: Enterovirus A71 / Strain: B2-11316-86

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Component #4: protein, VP3

ProteinName: VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.540332 kDa
SourceSpecies: Enterovirus A71 / Strain: B2-11316-86

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Component #5: protein, VP4

ProteinName: VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.501162 kDa
SourceSpecies: Enterovirus A71 / Strain: B2-11316-86

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Component #6: ligand, SPHINGOSINE

LigandName: SPHINGOSINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.299492 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen 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: 44 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: 152476
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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