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- PDB-6lat: The cryo-EM structure of HEV VLP -

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Basic information

Entry
Database: PDB / ID: 6lat
TitleThe cryo-EM structure of HEV VLP
ComponentsProtein ORF2
KeywordsVIRUS LIKE PARTICLE / HEV / T=1
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
Elongation Factor Tu (Ef-tu); domain 3 - #190 / Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / : / Structural protein 2 second domain / : / Structural protein 2 C-terminal domain / Jelly Rolls - #20 / Elongation Factor Tu (Ef-tu); domain 3 / Viral coat protein subunit ...Elongation Factor Tu (Ef-tu); domain 3 - #190 / Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / : / Structural protein 2 second domain / : / Structural protein 2 C-terminal domain / Jelly Rolls - #20 / Elongation Factor Tu (Ef-tu); domain 3 / Viral coat protein subunit / Jelly Rolls / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pro-secreted protein ORF2 / Pro-secreted protein ORF2
Similarity search - Component
Biological speciesHepatitis E virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZheng, Q. / He, M. / Li, S.
Funding support China, 2items
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, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Protein ORF2


Theoretical massNumber of molelcules
Total (without water)51,3031
Polymers51,3031
Non-polymers00
Water00
1
A: Protein ORF2
x 60


Theoretical massNumber of molelcules
Total (without water)3,078,18460
Polymers3,078,18460
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22090 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Protein ORF2
x 5


  • icosahedral pentamer
  • 257 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)256,5155
Polymers256,5155
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Protein ORF2
x 6


  • icosahedral 23 hexamer
  • 308 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)307,8186
Polymers307,8186
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Protein ORF2 / HEV p495 protein


Mass: 51303.062 Da / Num. of mol.: 1 / Mutation: P162S,N200S,A511S,L569I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P6DD72, UniProt: P33426*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hepatitis E virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Hepatitis E virus
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13759 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0123556
ELECTRON MICROSCOPYf_angle_d1.1274862
ELECTRON MICROSCOPYf_dihedral_angle_d7.6412121
ELECTRON MICROSCOPYf_chiral_restr0.064577
ELECTRON MICROSCOPYf_plane_restr0.008627

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