8PMZ | pdb_00008pmz

HEV gt3 P domain in complex with glycan-insensitive nAb p61.15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.257 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PMZ

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 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.

Macromolecule Content 

  • Total Structure Weight: 100.62 kDa 
  • Atom Count: 6,163 
  • Modeled Residue Count: 758 
  • Deposited Residue Count: 932 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pro-secreted protein ORF2
A, C
211Paslahepevirus balayaniMutation(s): 0 
UniProt
Find proteins for C4B4T9 (Hepatitis E virus)
Explore C4B4T9 
Go to UniProtKB:  C4B4T9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4B4T9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv_p61.15
B, D
255Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B3P

Query on B3P



Download:Ideal Coordinates CCD File
E [auth A],
F [auth C]
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.257 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.59α = 90
b = 178.77β = 90
c = 49.66γ = 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