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 9Z5U | pdb_00009z5u

Cryo-EM structure of a soluble HCV E1E2 antigen in complex with AT1211 fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9Z5U

This is version 1.1 of the entry. See complete history. 

Literature

Structure-based design of stable recombinant hepatitis C virus E1E2 heterodimers.

Capella-Pujol, J., Mulder, F., Cannac, F., Peters, S., Newby, M.L., Poniman, M., Zon, I., Olijhoek, W., Beaumont, T., Crispin, M., Ward, A.B., Schinkel, J., Sanders, R.W., Sliepen, K.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-75744-9
  • Primary Citation Related Structures: 
    9Z5U

  • PubMed Abstract: 

    Hepatitis C virus (HCV) affects 47 million people and causes 239,000 deaths annually, yet no vaccine is on the horizon. Generating a stable native-like mimic of the envelope complex E1E2, the only target for known neutralizing antibodies, is an important aim for HCV vaccine development. Starting from a recombinant E1E2 design that utilizes a leucine zipper for proper folding, we used an iterative structure-based design approach to engineer antigens with at least 100-fold stronger binding to conformational antibodies and increased thermal stability. These new E1E2 designs facilitate production of native-like E1E2 antigens based on strains from different HCV genotypes and enable the generation of a recombinant E1E2 antigen design that lacks the immunogenic leucine zipper. A cryo-EM structure of one of the stabilized E1E2 antigens in complex with neutralizing antibody AT1211 provides atomic-level insights into an atypical epitope on the E2 subunit. Finally, immunogenicity studies in rabbits with adjuvanted E1E2 proteins show that immunogen stabilization alone does do not enhance serum neutralization breadth, but that removing the leucine zipper does increase homologous serum neutralization.


  • Organizational Affiliation: 
    • Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.

Macromolecule Content 

  • Total Structure Weight: 113.96 kDa 
  • Atom Count: 3,348 
  • Modeled Residue Count: 423 
  • Deposited Residue Count: 1,032 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
sE1E2589Orthohepacivirus hominisMutation(s): 0 
UniProt
Find proteins for A0A159UHX2 (Orthohepacivirus hominis)
Explore A0A159UHX2 
Go to UniProtKB:  A0A159UHX2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A159UHX2
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AT1211 Heavy ChainB [auth H]229Homo sapiensMutation(s): 0 
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Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
AT1211 Light ChainC [auth L]214Homo sapiensMutation(s): 0 
Entity Groups
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references