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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0863 | |||||||||
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Title | The cryo-EM structure of HEV VLP | |||||||||
![]() | The cryo-EM structure of HEV VLP | |||||||||
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![]() | HEV / virus like particle / T=1 | |||||||||
Function / homology | ![]() T=1 icosahedral viral capsid / host cell endoplasmic reticulum / host cell Golgi apparatus / host cell surface / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / cell surface / RNA binding ...T=1 icosahedral viral capsid / host cell endoplasmic reticulum / host cell Golgi apparatus / host cell surface / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / cell surface / RNA binding / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Zheng Q / He M / Li S | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Viral neutralization by antibody-imposed physical disruption. Authors: Qingbing Zheng / Jie Jiang / Maozhou He / Zizheng Zheng / Hai Yu / Tingting Li / Wenhui Xue / Zimin Tang / Dong Ying / Zekai Li / Shuo Song / Xinlin Liu / Kaihang Wang / Zhiqing Zhang / ...Authors: Qingbing Zheng / Jie Jiang / Maozhou He / Zizheng Zheng / Hai Yu / Tingting Li / Wenhui Xue / Zimin Tang / Dong Ying / Zekai Li / Shuo Song / Xinlin Liu / Kaihang Wang / Zhiqing Zhang / Daning Wang / Yingbin Wang / Xiaodong Yan / Qinjian Zhao / Jun Zhang / Ying Gu / Shaowei Li / Ningshao Xia / ![]() ![]() Abstract: In adaptive immunity, organisms produce neutralizing antibodies (nAbs) to eliminate invading pathogens. Here, we explored whether viral neutralization could be attained through the physical ...In adaptive immunity, organisms produce neutralizing antibodies (nAbs) to eliminate invading pathogens. Here, we explored whether viral neutralization could be attained through the physical disruption of a virus upon nAb binding. We report the neutralization mechanism of a potent nAb 8C11 against the hepatitis E virus (HEV), a nonenveloped positive-sense single-stranded RNA virus associated with abundant acute hepatitis. The 8C11 binding flanks the protrusion spike of the HEV viruslike particles (VLPs) and leads to tremendous physical collision between the antibody and the capsid, dissociating the VLPs into homodimer species within 2 h. Cryo-electron microscopy reconstruction of the dissociation intermediates at an earlier (15-min) stage revealed smeared protrusion spikes and a loss of icosahedral symmetry with the capsid core remaining unchanged. This structural disruption leads to the presence of only a few native HEV virions in the ultracentrifugation pellet and exposes the viral genome. Conceptually, we propose a strategy to raise collision-inducing nAbs against single spike moieties that feature in the context of the entire pathogen at positions where the neighboring space cannot afford to accommodate an antibody. This rationale may facilitate unique vaccine development and antimicrobial antibody design. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 227.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
Images | ![]() | 113.5 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6latMC ![]() 0861C ![]() 0866C ![]() 6lb0C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | The cryo-EM structure of HEV VLP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : Hepatitis E virus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Hepatitis E virus
Supramolecule | Name: Hepatitis E virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12461 / Sci species name: Hepatitis E virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Protein ORF2
Macromolecule | Name: Protein ORF2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 51.303062 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GAILRRQYNL STSPLTSSVA TGTNLVLYAA PLSSLLPLQD GTNTHIMATE ASNYAQYRVA RATIRYRPLV PSAVGGYAIS ISFWPQTTT TPTSVDMNSI TSTDVRILVQ PGIASELVIP SERLHYRNQG WRSVETSGVA EEEATSGLVM LCIHGSPVNS Y TNTPYTGA ...String: GAILRRQYNL STSPLTSSVA TGTNLVLYAA PLSSLLPLQD GTNTHIMATE ASNYAQYRVA RATIRYRPLV PSAVGGYAIS ISFWPQTTT TPTSVDMNSI TSTDVRILVQ PGIASELVIP SERLHYRNQG WRSVETSGVA EEEATSGLVM LCIHGSPVNS Y TNTPYTGA LGLLDFALEL EFRNLTPGNT NTRVSRYSST ARHRLRRGAD GTAELTTTAA TRFMKDLYFT STNGVGEIGR GI ALTLFNL ADTLLGGLPT ELISSAGGQL FYSRPVVSAN GEPTVKLYTS VENAQQDKGI AIPHDIDLGE SRVVIQDYDN QHE QDRPTP SPAPSRPFSV LRANDVLWLS LTAAEYDQST YGSSTGPVYV SDSVTLVNVA TGAQAVSRSL DWTKVTLDGR PLST IQQYS KTFFVLPLRG KLSFWEAGTT KAGYPYNYNT TASDQILVEN AAGHRVAIST YTTSLGAGPV SISAVAVLAP HS UniProtKB: Pro-secreted protein ORF2 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.0 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13759 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: ANGULAR RECONSTITUTION |