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- PDB-6ad0: The structure of CVA10 mature virion in complex with Fab 2G8 -

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Entry
Database: PDB / ID: 6ad0
TitleThe structure of CVA10 mature virion in complex with Fab 2G8
Components
  • VH of Fab 2G8
  • VL of Fab 2G8
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS/IMMUNE SYSTEM / CVA10 / immune complex / neutralizing antibody / VIRUS / VIRUS-IMMUNE SYSTEM complex
Function / homologyPeptidase C3, picornavirus core protein 2A / Viral coat protein subunit / Poliovirus 3A protein-like / 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 ...Peptidase C3, picornavirus core protein 2A / Viral coat protein subunit / Poliovirus 3A protein-like / 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 C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 superfamily / picornavirus capsid protein / 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 / P-loop containing nucleoside triphosphate hydrolase / 3C cysteine protease (picornain 3C) / T=pseudo3 icosahedral viral capsid / 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 / 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 / Genome polyprotein / Polyprotein
Function and homology information
Specimen sourceMus musculus (house mouse)
Coxsackievirus A10
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsZhu, R. / Zheng, Q.B. / Xu, L.F. / Cui, Y.X. / Li, S.W. / Yan, X.D. / Zhou, Z.H. / Cheng, T.
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 Kong / Jun Zhang / Timothy S Baker / Xiaodong Yan / Z Hong Zhou / Tong Cheng / Ningshao Xia
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 28, 2018 / Release: Nov 21, 2018

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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
L: VL of Fab 2G8
H: VH of Fab 2G8
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4027
Polyers120,1026
Non-polymers2991
Water0
1
L: VL of Fab 2G8
H: VH of Fab 2G8
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,224,116420
Polyers7,206,147360
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area (Å2)25040
ΔGint (kcal/M)-123
Surface area (Å2)45270
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
L: VL of Fab 2G8
H: VH of Fab 2G8
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 602 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)602,01035
Polyers600,51230
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
L: VL of Fab 2G8
H: VH of Fab 2G8
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 722 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)722,41242
Polyers720,61536
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

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Components

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Protein/peptide , 6 types, 6 molecules LHABCD

#1: Protein/peptide VL of Fab 2G8


Mass: 12391.881 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse)
#2: Protein/peptide VH of Fab 2G8


Mass: 13149.508 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide VP1


Mass: 33159.230 Da / Num. of mol.: 1 / Source: (natural) Coxsackievirus A10 / References: UniProt: A0A1V0FT21
#4: Protein/peptide VP2


Mass: 27808.133 Da / Num. of mol.: 1 / Source: (natural) Coxsackievirus A10 / References: UniProt: A0A1V0FT21
#5: Protein/peptide VP3


Mass: 26129.588 Da / Num. of mol.: 1 / Source: (natural) Coxsackievirus A10 / References: UniProt: A0A1V0FT21
#6: Protein/peptide VP4


Mass: 7464.104 Da / Num. of mol.: 1 / Source: (natural) Coxsackievirus A10 / References: UniProt: Q75Q92

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Formula: C18H37NO2 / Sphingosine

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: CVA10 mature virion in complex with Fab 2G8 / Type: VIRUS / Entity ID: 1, 2, 3, 4, 5, 6
Source (natural)Organism: Coxsackievirus A10
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus 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
MicroscopyMicroscope model: 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

CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 36555 / Symmetry type: POINT

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