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Yorodumi- EMDB-9635: The structure of Enterovirus D68 A-particle triggered by an unkno... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9635 | |||||||||
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Title | The structure of Enterovirus D68 A-particle triggered by an unknown stimulus | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Enterovirus D68 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Zheng QB / Zhu R / Xu LF / He MZ / Yan XD / Cheng T / Li SW | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9635.map.gz | 325 MB | EMDB map data format | |
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Header (meta data) | emd-9635-v30.xml emd-9635.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9635_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_9635.png | 251.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9635 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9635 | HTTPS FTP |
-Related structure data
Related structure data | 9629C 9631C 9632C 9633C 9634C 9636C 6aj0C 6aj2C 6aj3C 6aj7C 6aj9C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9635.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.128 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Enterovirus D68
Entire | Name: Enterovirus D68 |
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Components |
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-Supramolecule #1: Enterovirus D68
Supramolecule | Name: Enterovirus D68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 42789 / Sci species name: Enterovirus D68 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: Enterovirus D68 |
Sequence | String: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSAAQADKNF FKWTINTRSF VQLRRKLELF TYLRFDAEIT ILTTVAVNGS GNNTYVGLPD LTLQAMFVPT GALTPEKQDS FHWQSGSNAS ...String: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSAAQADKNF FKWTINTRSF VQLRRKLELF TYLRFDAEIT ILTTVAVNGS GNNTYVGLPD LTLQAMFVPT GALTPEKQDS FHWQSGSNAS VFFKISDPPA RITIPFMCIN SAYSVFYDGF AGFEKNGLYG INPADTIGNL CVRIVNEHQP VGFTVTVRVY MKPKHIKAWA PRPPRTLPYM SIANANYKGK ERAPNALNAI IGNRDSVKTM PHNIV |
-Macromolecule #2: VP2
Macromolecule | Name: VP2 / type: other / ID: 2 / Classification: other |
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Source (natural) | Organism: Enterovirus D68 |
Sequence | String: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETGSTGWWW KLPDALNNIG MFGQNVQHHY LYRSGFLIHV QCNATKFHQG ALLVVAIPEH QRGAHNTNTS PGFDDIMKGE EGGTFNHPYV LDDGTSLACA ...String: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETGSTGWWW KLPDALNNIG MFGQNVQHHY LYRSGFLIHV QCNATKFHQG ALLVVAIPEH QRGAHNTNTS PGFDDIMKGE EGGTFNHPYV LDDGTSLACA TIFPHQWINL RTNNSATIVL PWMNAAPMDF PLRHNQWTLA IIPVVPLGTR TTSSMVPITV SIAPMCCEFN GLRHAITQ |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: other / ID: 3 / Classification: other |
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Source (natural) | Organism: Enterovirus D68 |
Sequence | String: GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQL DGPLRNTLVG NISRYYTHWS GSLEMTFMFC GSFMATGKLI LCYTPPGGSC PTTRETAMLG THIVWDFGLQ SSVTLIIPWI ...String: GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQL DGPLRNTLVG NISRYYTHWS GSLEMTFMFC GSFMATGKLI LCYTPPGGSC PTTRETAMLG THIVWDFGLQ SSVTLIIPWI SGSHYRMFNN DAKSTNANVG YVTCFMQTNL IVPSESSDTC SLIGFIAAKD DFSLRLMRDS PDIGQLDHLH AAEAAYQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |