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- PDB-6aj2: The structure of ICAM-5 triggered Enterovirus D68 virus A-particle -

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Basic information

Entry
Database: PDB / ID: 6aj2
TitleThe structure of ICAM-5 triggered Enterovirus D68 virus A-particle
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
KeywordsVIRUS / Enterovirus D68 / ICAM-5 / A-paticle
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 / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / 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 / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphate phosphatase / viral capsid / protein complex oligomerization / induction by virus of host autophagy / RNA-directed RNA polymerase / ion channel activity / suppression by virus of host gene expression / peptidase activity / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / viral process / RNA binding / membrane / ATP binding
RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded RNA virus / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein VP4 / Picornavirus capsid / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan ...RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded RNA virus / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein VP4 / Picornavirus capsid / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / AAA+ ATPase domain / Poliovirus 3A protein-like / Poliovirus core protein 3a, soluble domain / picornavirus capsid protein / P-loop containing nucleoside triphosphate hydrolase / Picornavirus coat protein VP4 superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Jelly Rolls - #20 / Jelly Rolls / Sandwich / Mainly Beta
Genome polyprotein / Polyprotein
Biological speciesEnterovirus D68
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsZheng, Q.B. / Zhu, R. / Xu, L.F. / He, M.Z. / Yan, X.D. / Cheng, T. / Li, S.W.
Funding support China, United States, 11items
OrganizationGrant numberCountry
National Natural Science Foundation of China81401669 China
National Institutes of Health/National Institute of General Medical SciencesR37-GM33050 United States
National Institutes of Health/National Institute of General Medical SciencesGM071940 United States
National Institutes of Health/National Institute of General Medical Sciences1U24GM116792 United States
National Institutes of Health/National Institute of Dental and Craniofacial ResearchDE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI094386 United States
National Institutes of Health/National Center for Research Resources1S10RR23057 United States
National Science Foundation (United States)DBI-1338135 United States
National Science Foundation (United States)DMR-1548924 United States
National Science Foundation (United States)DBI-1338135 United States
National Science Foundation (United States)DMR-1548924 United States
CitationJournal: Nat Microbiol / Year: 2019
Title: Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization.
Authors: Qingbing Zheng / Rui Zhu / Longfa Xu / Maozhou He / Xiaodong Yan / Dongxiao Liu / Zhichao Yin / Yangtao Wu / Yongchao Li / Lisheng Yang / Wangheng Hou / Shuxuan Li / Zizhen Li / Zhenqin Chen ...Authors: Qingbing Zheng / Rui Zhu / Longfa Xu / Maozhou He / Xiaodong Yan / Dongxiao Liu / Zhichao Yin / Yangtao Wu / Yongchao Li / Lisheng Yang / Wangheng Hou / Shuxuan Li / Zizhen Li / Zhenqin Chen / Zhihai Li / Hai Yu / Ying Gu / Jun Zhang / Timothy S Baker / Z Hong Zhou / Barney S Graham / Tong Cheng / Shaowei Li / Ningshao Xia /
Abstract: Enterovirus D68 (EV-D68) undergoes structural transformation between mature, cell-entry intermediate (A-particle) and empty forms throughout its life cycle. Structural information for the various ...Enterovirus D68 (EV-D68) undergoes structural transformation between mature, cell-entry intermediate (A-particle) and empty forms throughout its life cycle. Structural information for the various forms and antibody-bound capsids will facilitate the development of effective vaccines and therapeutics against EV-D68 infection, which causes childhood respiratory and paralytic diseases worldwide. Here, we report the structures of three EV-D68 capsid states representing the virus at major phases. We further describe two original monoclonal antibodies (15C5 and 11G1) with distinct structurally defined mechanisms for virus neutralization. 15C5 and 11G1 engage the capsid loci at icosahedral three-fold and five-fold axes, respectively. To block viral attachment, 15C5 binds three forms of capsids, and triggers mature virions to transform into A-particles, mimicking engagement by the functional receptor ICAM-5, whereas 11G1 exclusively recognizes the A-particle. Our data provide a structural and molecular explanation for the transition of picornavirus capsid conformations and demonstrate distinct mechanisms for antibody-mediated neutralization.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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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: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)87,3833
Polymers87,3833
Non-polymers00
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,242,981180
Polymers5,242,981180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area12600 Å2
ΔGint-74 kcal/mol
Surface area32940 Å2
2


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


  • icosahedral pentamer
  • 437 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)436,91515
Polymers436,91515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 6


  • icosahedral 23 hexamer
  • 524 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)524,29818
Polymers524,29818
Non-polymers00
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 Capsid protein VP1 / / Virion protein 1


Mass: 32673.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus D68
References: UniProt: A0A097F8Q2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein Capsid protein VP2 / / Virion protein 2


Mass: 27567.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus D68 / References: UniProt: A0A0A7X639, UniProt: A0A097F8Q2*PLUS
#3: Protein Capsid protein VP3 / / Virion protein 3


Mass: 27142.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus D68 / References: UniProt: A0A097F8Q2*PLUS

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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 D / Type: VIRUS / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Enterovirus D
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9625 / Symmetry type: POINT

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