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- PDB-6acu: The structure of CVA10 virus mature virion -

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Basic information

Entry
Database: PDB / ID: 6acu
TitleThe structure of CVA10 virus mature virion
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / CVA10 / Mature virion / Icosahedral
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 / 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 / RNA binding / membrane / ATP binding
Picornavirus coat protein VP4 / Poliovirus 3A protein-like / Peptidase S1, PA clan / Peptidase C3, picornavirus core protein 2A / Peptidase C3A/C3B, picornaviral / AAA+ ATPase domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid ...Picornavirus coat protein VP4 / Poliovirus 3A protein-like / Peptidase S1, PA clan / Peptidase C3, picornavirus core protein 2A / Peptidase C3A/C3B, picornaviral / AAA+ ATPase domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 superfamily / picornavirus capsid protein / Picornavirus coat protein (VP4) / Picornavirus 2B protein / RNA-directed RNA polymerase, catalytic domain / Jelly Rolls - #20 / Jelly Rolls / Sandwich / Mainly Beta
Genome polyprotein / Polyprotein
Biological speciesCoxsackievirus A10
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCui, Y.X. / Zheng, Q.B. / Zhu, R. / Xu, L.F. / Li, S.W. / Yan, X.D. / Zhou, Z.H. / Cheng, T.
Funding support China, United States, 9items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670933 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 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 Institutes of Health/National Institute of General Medical Sciences1U24GM116792 United States
National Science Foundation (United States)DBI-1338135 United States
National Science Foundation (United States)DMR-1548924 United States
CitationJournal: Sci Adv / Year: 2018
Title: Discovery and structural characterization of a therapeutic antibody against coxsackievirus A10.
Authors: Rui Zhu / Longfa Xu / Qingbing Zheng / Yanxiang Cui / Shaowei Li / Maozhou He / Zhichao Yin / Dongxiao Liu / Shuxuan Li / Zizhen Li / Zhenqin Chen / Hai Yu / Yuqiong Que / Che Liu / Zhibo ...Authors: Rui Zhu / Longfa Xu / Qingbing Zheng / Yanxiang Cui / Shaowei Li / Maozhou He / Zhichao Yin / Dongxiao Liu / Shuxuan Li / Zizhen Li / Zhenqin Chen / Hai Yu / Yuqiong Que / Che Liu / Zhibo Kong / Jun Zhang / Timothy S Baker / Xiaodong Yan / Z Hong Zhou / Tong Cheng / Ningshao Xia /
Abstract: Coxsackievirus A10 (CVA10) recently emerged as a major pathogen of hand, foot, and mouth disease and herpangina in children worldwide, and lack of a vaccine or a cure against CVA10 infections has ...Coxsackievirus A10 (CVA10) recently emerged as a major pathogen of hand, foot, and mouth disease and herpangina in children worldwide, and lack of a vaccine or a cure against CVA10 infections has made therapeutic antibody identification a public health priority. By targeting a local isolate, CVA10-FJ-01, we obtained a potent antibody, 2G8, against all three capsid forms of CVA10. We show that 2G8 exhibited both 100% preventive and 100% therapeutic efficacy against CVA10 infection in mice. Comparisons of the near-atomic cryo-electron microscopy structures of the three forms of CVA10 capsid and their complexes with 2G8 Fab reveal that a single Fab binds a border region across the three capsid proteins (VP1 to VP3) and explain 2G8's remarkable cross-reactivities against all three capsid forms. The atomic structures of this first neutralizing antibody of CVA10 should inform strategies for designing vaccines and therapeutics against CVA10 infections.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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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)94,8615
Polymers94,5614
Non-polymers2991
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,691,633300
Polymers5,673,663240
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
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)474,30325
Polymers472,80520
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
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)569,16330
Polymers567,36624
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 VP1


Mass: 33159.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10 / References: UniProt: A0A1V0FT21
#2: Protein VP2


Mass: 27808.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10 / References: UniProt: A0A1V0FT21
#3: Protein VP3


Mass: 26129.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10 / References: UniProt: A0A1V0FT21
#4: Protein VP4


Mass: 7464.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10 / References: UniProt: Q75Q92, UniProt: A0A1V0FT21*PLUS
#5: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


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

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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: Coxsackievirus A10 / Type: VIRUS / Entity ID: 1, 2, 3, 4 / Source: NATURAL
Source (natural)Organism: Coxsackievirus A10
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)

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Processing

EM softwareName: Gctf / Category: CTF correction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17092 / Symmetry type: POINT

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