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- PDB-6dij: Structure of the EVA71 strain 11316 capsid -

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Basic information

Entry
Database: PDB / ID: 6dij
TitleStructure of the EVA71 strain 11316 capsid
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / tryptophan dendrimers / EV-A71 / 5-fold vertex / Cryo-EM
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
Specimen sourceEnterovirus A71
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSun, L. / Lee, H. / Thibaut, H.J. / Rivero-Buceta, E. / Martinez-Gualda, B. / Delang, L. / Leyssen, P. / Gago, F. / San-Felix, A. / Hafenstein, S. / Mirabelli, C. / Neyts, J.
Funding support1件
OrganizationGrant numberCountry
European Regional Development Fund
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 Report
SummaryFull reportAbout validation report
DateDeposition: May 23, 2018 / Release: May 1, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 1, 2019Structure modelrepositoryInitial release
1.1May 22, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0365
Polymers93,7374
Non-polymers2991
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,642,165300
Polymers5,624,195240
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 470 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)470,18025
Polymers468,68320
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 564 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)564,21630
Polymers562,42024
Non-polymers1,7976
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein/peptide VP1


Mass: 32748.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / Strain: B2-11316-86 / References: UniProt: D4QGA8
#2: Protein/peptide VP2


Mass: 26946.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / Strain: B2-11316-86 / References: UniProt: I6W7A3
#3: Protein/peptide VP3


Mass: 26540.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / Strain: B2-11316-86 / References: UniProt: A0A0E3SXU7
#4: Protein/peptide VP4


Mass: 7501.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / Strain: B2-11316-86 / References: UniProt: E9RGA0
#5: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Sphingosine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Enterovirus A71Enterovirus 71 / Type: VIRUS / Entity ID: 1, 2, 3, 4 / Source: NATURAL
Source (natural)Organism: Enterovirus A71
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 44 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152476 / Symmetry type: POINT

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