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- PDB-6aj0: The structure of Enterovirus D68 mature virion -

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Basic information

Entry
Database: PDB / ID: 6aj0
TitleThe structure of Enterovirus D68 mature virion
Components
  • Capsid protein VP3
  • Capsid protein VP4
  • Viral protein 1
  • Virion protein 2Virus
KeywordsVIRUS / Enterovirus D68 / mature virion
Function / homologyPeptidase C3, picornavirus core protein 2A / Picornavirus coat protein VP4 superfamily / 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 / Picornavirus coat protein VP4 superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus 3A protein-like / Poliovirus core protein 3a, soluble domain / Helicase, superfamily 3, single-stranded RNA virus / Picornavirus coat protein (VP4) / picornavirus capsid protein / 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. / RNA helicase / Poliovirus 3A protein like / Picornavirus core protein 2A / Picornavirus 2B protein / 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 / transcription, DNA-templated / RNA binding / membrane / ATP binding / Genome polyprotein / Polyprotein / Polyprotein
Function and homology information
Specimen sourceEnterovirus D68
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 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: 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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 25, 2018 / Release: Nov 7, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 7, 2018Structure modelrepositoryInitial release
1.1Nov 21, 2018Structure modelData collection / Database referencescitation / citation_author_citation.pdbx_database_id_PubMed

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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
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Viral protein 1
B: Virion protein 2
C: Capsid protein VP3
D: Capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)94,8514
Polyers94,8514
Non-polymers00
Water0
1
A: Viral protein 1
B: Virion protein 2
C: Capsid protein VP3
D: Capsid protein VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,691,070240
Polyers5,691,070240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area (Å2)18960
ΔGint (kcal/M)-98
Surface area (Å2)35130
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Viral protein 1
B: Virion protein 2
C: Capsid protein VP3
D: Capsid protein VP4
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)474,25620
Polyers474,25620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Viral protein 1
B: Virion protein 2
C: Capsid protein VP3
D: Capsid protein VP4
x 6


  • icosahedral 23 hexamer
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)569,10724
Polyers569,10724
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 Viral protein 1 /


Mass: 32673.035 Da / Num. of mol.: 1 / Source: (natural) Enterovirus D68 / References: UniProt: A0A097F8Q2
#2: Protein/peptide Virion protein 2 / Virus


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
#4: Protein/peptide Capsid protein VP4 / / Virion protein 4


Mass: 7468.157 Da / Num. of mol.: 1 / Source: (natural) Enterovirus D68 / References: UniProt: E7FM39

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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: Coxsackievirus A10 / Type: VIRUS / Entity ID: 1, 2, 3, 4 / Source: NATURAL
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

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 11938 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00950552
ELECTRON MICROSCOPYf_angle_d0.94668872
ELECTRON MICROSCOPYf_dihedral_angle_d6.05329984
ELECTRON MICROSCOPYf_chiral_restr0.0637752
ELECTRON MICROSCOPYf_plane_restr0.0088896

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