8PMX | pdb_00008pmx

rat HEV P domain in complex with glycan-sensitive nAb p60.12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.92 Å
  • R-Value Free: 
    0.361 (Depositor), 0.370 (DCC) 
  • R-Value Work: 
    0.300 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.304 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Broadly neutralizing antibodies isolated from HEV convalescents confer protective effects in human liver-chimeric mice.

Ssebyatika, G.Dinkelborg, K.Stroh, L.J.Hinte, F.Corneillie, L.Hueffner, L.Guzman, E.M.Nankya, P.L.Pluckebaum, N.Fehlau, L.Garn, J.Meyer, N.Prallet, S.Mehnert, A.K.Kraft, A.R.M.Verhoye, L.Jacobsen, C.Steinmann, E.Wedemeyer, H.Viejo-Borbolla, A.Dao Thi, V.L.Pietschmann, T.Lutgehetmann, M.Meuleman, P.Dandri, M.Krey, T.Behrendt, P.

(2025) Nat Commun 16: 1995-1995

  • DOI: https://doi.org/10.1038/s41467-025-57182-1
  • Primary Citation of Related Structures:  
    8PMW, 8PMX, 8PMY, 8PMZ, 8PN0

  • PubMed Abstract: 

    Hepatitis E virus (HEV) causes 3.3 million symptomatic cases and 44,000 deaths per year. Chronic infections can arise in immunocompromised individuals, and pregnant women may suffer from fulminant disease as a consequence of HEV infection. Despite these important implications for public health, no specific antiviral treatment has been approved to date. Here, we report combined functional, biochemical, and X-ray crystallographic studies that characterize the human antibody response in convalescent HEV patients. We identified a class of potent and broadly neutralizing human antibodies (bnAbs), targeting a quaternary epitope located at the tip of the HEV capsid protein pORF2 that contains an N-glycosylation motif and is conserved across members of the Hepeviridae. These glycan-sensitive bnAbs specifically recognize the non-glycosylated pORF2 present in infectious particles but not the secreted glycosylated form acting as antibody decoy. Our most potent bnAb protects human liver-chimeric mice from intraperitoneal HEV challenge and co-housing exposure. These results provide insights into the bnAb response to this important emerging pathogen and support the development of glycan-sensitive antibodies to combat HEV infection.


  • Organizational Affiliation
    • Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pro-secreted protein ORF2
A, B
165Hepatitis E virus rat/R63/DEU/2009Mutation(s): 0 
UniProt
Find proteins for E0XL23 (Hepatitis E virus rat/R63/DEU/2009)
Explore E0XL23 
Go to UniProtKB:  E0XL23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0XL23
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab p60.12-HCC [auth H]233Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab p60.12-LCD [auth L]217Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.92 Å
  • R-Value Free:  0.361 (Depositor), 0.370 (DCC) 
  • R-Value Work:  0.300 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.304 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.856α = 90
b = 112.856β = 90
c = 184.439γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Volkswagen FoundationGermany9A888

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2025-07-23
    Changes: Database references