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- EMDB-0861: The cryo-EM structure of HEV VLP in complex with Fab 3B6 -

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Basic information

Entry
Database: EMDB / ID: EMD-0861
TitleThe cryo-EM structure of HEV VLP in complex with Fab 3B6
Map data
SampleHepatitis E virus:
virus
Function / homology
Function and homology information


host cell surface / entry receptor-mediated virion attachment to host cell / host cell Golgi apparatus / T=1 icosahedral viral capsid / host cell endoplasmic reticulum / viral capsid / viral entry into host cell / host cell cytoplasm / structural molecule activity / RNA binding ...host cell surface / entry receptor-mediated virion attachment to host cell / host cell Golgi apparatus / T=1 icosahedral viral capsid / host cell endoplasmic reticulum / viral capsid / viral entry into host cell / host cell cytoplasm / structural molecule activity / RNA binding / extracellular region / identical protein binding / cytoplasm
Viral coat protein subunit / Hepatitis E virus structural protein 2
Protein ORF2 / Secreted protein ORF2
Biological speciesHepatitis E virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsZheng Q / He M / Jiang J / Li S
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China81571996 China
National Natural Science Foundation of China81871247 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
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
DepositionNov 13, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseDec 4, 2019-
UpdateJun 17, 2020-
Current statusJun 17, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0861.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 600 pix.
= 676.8 Å
1.13 Å/pix.
x 600 pix.
= 676.8 Å
1.13 Å/pix.
x 600 pix.
= 676.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density
Contour LevelBy AUTHOR: 0.0385 / Movie #1: 0.0385
Minimum - Maximum-0.09468393 - 0.1366986
Average (Standard dev.)0.000445055 (±0.007740099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 676.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z676.800676.800676.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0950.1370.000

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Supplemental data

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Sample components

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Entire Hepatitis E virus

EntireName: Hepatitis E virus / Number of components: 1

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Component #1: virus, Hepatitis E virus

VirusName: Hepatitis E virusOrthohepevirus A / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Hepatitis E virus
Source (engineered)Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1029
3D reconstructionResolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF

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