4PLK | pdb_00004plk

Hepatitis E Virus E2s domain (Genotype I) in complex with a neutralizing antibody 8G12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 
    0.296 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.264 (Depositor), 0.273 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural basis for the neutralization of hepatitis E virus by a cross-genotype antibody

Gu, Y.Tang, X.Zhang, X.Song, C.Zheng, M.Wang, K.Zhang, J.Ng, M.H.Hew, C.L.Li, S.Xia, N.Sivaraman, J.

(2015) Cell Res 25: 604-620

  • DOI: https://doi.org/10.1038/cr.2015.34
  • Primary Citation Related Structures: 
    4PLJ, 4PLK

  • PubMed Abstract: 

    Hepatitis E virus (HEV), a non-enveloped, positive-sense, single-stranded RNA virus, is a major cause of enteric hepatitis. Classified into the family Hepeviridae, HEV comprises four genotypes (genotypes 1-4), which belong to a single serotype. We describe a monoclonal antibody (mAb), 8G12, which equally recognizes all four genotypes of HEV, with ∼ 2.53-3.45 nM binding affinity. The mAb 8G12 has a protective, neutralizing capacity, which can significantly block virus infection in host cells. Animal studies with genotypes 1, 3 and 4 confirmed the cross-genotype neutralizing capacity of 8G12 and its effective prevention of hepatitis E disease. The complex crystal structures of 8G12 with the HEV E2s domain (the most protruded region of the virus capsid) of the abundant genotypes 1 and 4 were determined at 4.0 and 2.3 Å resolution, respectively. These structures revealed that 8G12 recognizes both genotypes through the epitopes in the E2s dimerization region. Structure-based mutagenesis and cell-model assays with virus-like particles identified several conserved residues (Glu549, Lys554 and Gly591) that are essential for 8G12 neutralization. Moreover, the epitope of 8G12 is identified as a key epitope involved in virus-host interactions. These findings will help develop a common strategy for the prevention of the most abundant form of HEV infection.


  • Organizational Affiliation
    • 1] State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, China [2] National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, Fujian 361005, China.

Macromolecule Content 

  • Total Structure Weight: 255.25 kDa 
  • Atom Count: 17,362 
  • Modeled Residue Count: 2,268 
  • Deposited Residue Count: 2,352 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid proteinA,
B,
G [auth E],
H [auth F]
147Paslahepevirus balayaniMutation(s): 0 
UniProt
Find proteins for L0L7P5 (Hepatitis E virus)
Explore L0L7P5 
Go to UniProtKB:  L0L7P5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0L7P5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
8G12 light chainC [auth L],
E [auth C],
I [auth K],
K [auth G]
212Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
8G12 heavy chainD [auth H],
F [auth D],
J,
L [auth I]
229Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free:  0.296 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.264 (Depositor), 0.273 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.196α = 90
b = 191.993β = 90.03
c = 192.584γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary