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- EMDB-0866: The cryo-EM structure of HEV VLP in complex with Fab 8C11 -

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Basic information

Entry
Database: EMDB / ID: EMD-0866
TitleThe cryo-EM structure of HEV VLP in complex with Fab 8C11
Map dataThe cryo-EM structure of HEV VLP in complex with Fab 8C11
Sample
  • Virus: Hepatitis E virus
    • Protein or peptide: Protein ORF2
KeywordsHEV / Neutralizing antibody / immune-complex / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


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
Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / : / Structural protein 2 second domain / : / Structural protein 2 C-terminal domain / Viral coat protein subunit
Similarity search - Domain/homology
Pro-secreted protein ORF2 / Pro-secreted protein ORF2
Similarity search - Component
Biological speciesHepatitis E virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZheng Q / He M / 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-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0335
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0335
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lb0
  • Surface level: 0.0335
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6lb0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_0866.png

Downloads & links

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Map

FileDownload / File: emd_0866.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM structure of HEV VLP in complex with Fab 8C11
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 460 pix.
= 518.88 Å		1.13 Å/pix.
x 460 pix.
= 518.88 Å		1.13 Å/pix.
x 460 pix.
= 518.88 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0335 / Movie #1: 0.0335
Minimum - Maximum-0.112300925 - 0.20071943
Average (Standard dev.)0.00074508716 (±0.00972499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 518.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z518.880518.880518.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-0.1120.2010.001

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Supplemental data

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Sample components

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Entire : Hepatitis E virus

EntireName: Hepatitis E virus
Components
  • Virus: Hepatitis E virus
    • Protein or peptide: Protein ORF2

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Supramolecule #1: Hepatitis E virus

SupramoleculeName: 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

MacromoleculeName: Protein ORF2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis E virus
Molecular weightTheoretical: 51.303062 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen 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 modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4259
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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