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- PDB-6aj3: The structure of Enterovirus D68 procapsid -

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Basic information

Entry
Database: PDB / ID: 6aj3
TitleThe structure of Enterovirus D68 procapsid
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
KeywordsVIRUS / Enterovirus D68 / procapsid
Function / homologyHelicase, superfamily 3, single-stranded RNA virus / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Picornavirus 2B protein / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus 3A protein-like ...Helicase, superfamily 3, single-stranded RNA virus / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Picornavirus 2B protein / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus 3A protein-like / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein VP4 / AAA+ ATPase domain / picornavirus capsid protein / 3C cysteine protease (picornain 3C) / Peptidase S1, PA clan / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA-directed RNA polymerase, catalytic domain / 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 / RNA dependent RNA polymerase / Peptidase C3, picornavirus core protein 2A / 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-triphosphatase / viral capsid / RNA-directed RNA polymerase / ion channel activity / induction by virus of host autophagy / suppression by virus of host gene expression / protein complex oligomerization / peptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / virion attachment to host cell / viral process / structural molecule activity / RNA binding / transcription, DNA-templated / membrane / ATP binding / Genome polyprotein / Polyprotein
Function and homology information
Specimen sourceEnterovirus D68
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsZheng, Q.B. / Zhu, R. / Xu, L.F. / He, M.Z. / Yan, X.D. / Cheng, T. / Li, S.W.
CitationJournal: Nat Microbiol / Year: 2018
Title: Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization
Authors: Zheng, Q.B. / Zhu, R. / Xu, L.F. / He, M.Z. / Yan, X.D. / Cheng, T. / Li, S.W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 26, 2018 / Release: Nov 7, 2018

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Structure visualization

Movie
  • 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
  • EMDB-9632
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  • Superimposition on EM map
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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
Polyers87,3833
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
Polyers5,242,981180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area (Å2)9760
ΔGint (kcal/M)-62
Surface area (Å2)27050
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
Polyers436,91515
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
Polyers524,29818
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

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Components

#1: Protein/peptide Capsid protein VP1 / / Virion protein 1


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


Mass: 27567.135 Da / Num. of mol.: 1 / Source: (natural) Enterovirus D68 / References: UniProt: A0A0A7X639
#3: Protein/peptide Capsid protein VP3 / / Virion protein 3


Mass: 27142.842 Da / Num. of mol.: 1 / Source: (natural) Enterovirus D68

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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: Enterovirus d / Type: VIRUS / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Enterovirus d
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

EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 13849 / Symmetry type: POINT

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