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- PDB-9fq3: HEV ORF2 protein in complex with Fabs Es1.114 and Es5.127 -

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Basic information

Entry
Database: PDB / ID: 9fq3
TitleHEV ORF2 protein in complex with Fabs Es1.114 and Es5.127
Components
  • Himan IgG antibody Es1.114 - Fab light chain
  • Human IgG antibody Es1.114 - Fab heavy chain
  • Human IgG antibody Es5.127 - Fab light chain
  • Secreted protein ORF2
  • human IgG antibody Es5.127 - Fab heavy chain
KeywordsVIRAL PROTEIN / Hepatitis E virus
Function / homology
Function and homology information


host cell endoplasmic reticulum / T=1 icosahedral viral capsid / host cell surface / host cell Golgi apparatus / host cell nucleus / structural molecule activity / RNA binding / extracellular region
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
Similarity search - Component
Biological speciesHepatitis E virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBaquero, E. / Molinos, L. / Mouquet, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HEV ORF2 protein in complex with Fabs Es1.114 and Es5.127
Authors: Molinos, L. / Baquero, E. / Mouquet, H.
History
DepositionJun 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted protein ORF2
B: Secreted protein ORF2
C: human IgG antibody Es5.127 - Fab heavy chain
D: Human IgG antibody Es5.127 - Fab light chain
E: human IgG antibody Es5.127 - Fab heavy chain
F: Human IgG antibody Es5.127 - Fab light chain
G: Human IgG antibody Es1.114 - Fab heavy chain
H: Himan IgG antibody Es1.114 - Fab light chain
I: Human IgG antibody Es1.114 - Fab heavy chain
J: Himan IgG antibody Es1.114 - Fab light chain


Theoretical massNumber of molelcules
Total (without water)298,49610
Polymers298,49610
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Secreted protein ORF2 / ORF2s


Mass: 52886.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus / Gene: ORF2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9YLQ9
#2: Antibody human IgG antibody Es5.127 - Fab heavy chain


Mass: 25675.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Human IgG antibody Es5.127 - Fab light chain


Mass: 22762.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Antibody Human IgG antibody Es1.114 - Fab heavy chain


Mass: 25456.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#5: Antibody Himan IgG antibody Es1.114 - Fab light chain


Mass: 22466.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
Has protein modificationY

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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: Ternary complex of the HEV ORF2 protein with the Fab fragments of the monoclonal antibodies Es5.127 and Es1.114
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207869 / Symmetry type: POINT
RefinementCross valid method: NONE

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