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Yorodumi- PDB-6aj9: The structure of Enterovirus D68 mature virion in complex with Fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aj9 | ||||||||||||||||||||||||||||||||||||
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Title | The structure of Enterovirus D68 mature virion in complex with Fab 15C5 and 11G1 | ||||||||||||||||||||||||||||||||||||
Components |
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Keywords | VIRUS / Enterovirus D68 / neutralizing antibody / Immune-complex | ||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / peptidase activity / host cell cytoplasm / virion attachment to host cell / structural molecule activity / proteolysis / cytoplasm Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | Mus musculus (house mouse) Enterovirus D68 | ||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||||||||||||||||||||
Authors | Zheng, Q.B. / Zhu, R. / Xu, L.F. / He, M.Z. / Yan, X.D. / Cheng, T. / Li, S.W. | ||||||||||||||||||||||||||||||||||||
Funding support | China, United States, 11items
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Citation | Journal: 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. | ||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6aj9.cif.gz | 203 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aj9.ent.gz | 165.9 KB | Display | PDB format |
PDBx/mmJSON format | 6aj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aj9_validation.pdf.gz | 948.3 KB | Display | wwPDB validaton report |
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Full document | 6aj9_full_validation.pdf.gz | 952.4 KB | Display | |
Data in XML | 6aj9_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 6aj9_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/6aj9 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/6aj9 | HTTPS FTP |
-Related structure data
Related structure data | 9634MC 9629C 9631C 9632C 9633C 9635C 9636C 6aj0C 6aj2C 6aj3C 6aj7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
-Capsid protein ... , 3 types, 3 molecules ABC
#5: Protein | Mass: 32673.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus D68 / References: UniProt: A0A097F8Q2 |
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#6: Protein | 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 |
#7: Protein | Mass: 27142.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus D68 / References: UniProt: A0A097F8Q2*PLUS |
-Antibody , 4 types, 4 molecules EDLH
#1: Antibody | Mass: 12625.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 13517.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Antibody | Mass: 11656.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#4: Antibody | Mass: 13027.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Enterovirus D68 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Enterovirus D68 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software | Name: RELION / Version: 2 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING ONLY |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102512 / Symmetry type: POINT |