8QP6 | pdb_00008qp6

Crystal structure of Hepatitis C Virus E1 glycoprotein epitope 314-324 scaffold design 1W4K_08 in complex with neutralizing antibody F(ab) fragment IGH526

• PDB DOI: https://doi.org/10.2210/pdb8QP6/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Pyrobaculum aerophilum, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2023-09-30 Released: 2024-10-09 
• Deposition Author(s): Nagarathinam, K., Krey, T.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.273 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Epitope-focused immunogens targeting the hepatitis C virus glycoproteins induce broadly neutralizing antibodies.

Nagarathinam, K., Scheck, A., Labuhn, M., Stroh, L.J., Herold, E., Veselkova, B., Tune, S., Cramer, J.T., Rosset, S., Vollers, S.S., Bankwitz, D., Ballmaier, M., Boning, H., Roth, E., Khera, T., Ahsendorf-Abidi, H.P., Dittrich-Breiholz, O., Obleser, J., Nassal, M., Jack, H.M., Pietschmann, T., Correia, B.E., Krey, T.

(2024) Sci Adv 10: eado2600-eado2600

• PubMed: 39642219 
• DOI: https://doi.org/10.1126/sciadv.ado2600
• Primary Citation of Related Structures:  
  8QP6, 8QP7


• PubMed Abstract: 
  

  Hepatitis C virus (HCV) infection causes ~290,000 annual human deaths despite the highly effective antiviral treatment available. Several viral immune evasion mechanisms have hampered the development of an effective vaccine against HCV, among them the remarkable conformational flexibility within neutralization epitopes in the HCV antigens. Here, we report the design of epitope-focused immunogens displaying two distinct HCV cross-neutralization epitopes. We show that these immunogens induce a pronounced, broadly neutralizing antibody response in laboratory and transgenic human antibody mice. Monoclonal human antibodies isolated from immunized human antibody mice specifically recognized the grafted epitopes and neutralized four diverse HCV strains. Our results highlight a promising strategy for developing HCV immunogens and provide an encouraging paradigm for targeting structurally flexible epitopes to improve the induction of neutralizing antibodies.

---

Organizational Affiliation: 
• Institute of Biochemistry, Center of Structural and Cell Biology in Medicine, University of Lübeck, 23562 Lübeck, Germany.
Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland.
Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland.
Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany.
Institute of Virology, Hannover Medical School, 30625 Hannover, Germany.
Department of Psychology, University of Lübeck, 23562 Lübeck, Germany.
Center of Brain, Behavior, and Metabolism, University of Lübeck, 23562 Lübeck, Germany.
Central Research Facility Cell Sorting, Hannover Medical School, 30625 Hannover, Germany.
Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany.
Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany.
Department of Internal Medicine 2/Molecular Biology, University Hospital Freiburg, 79106 Freiburg, Germany.
German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany.
Excellence Cluster 2155 RESIST, Hannover Medical School, 30625 Hannover, Germany.
German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, 38124 Braunschweig, Germany.
Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A4B4C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B2C2D1E1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 435.33 kDa 
• Atom Count: 13,211 
• Modeled Residue Count: 1,822 
• Deposited Residue Count: 4,128 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1W4K_08	A, C [auth G], E [auth D], J	60	Pyrobaculum aerophilum	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F(ab) IGH526	B, D [auth C], F [auth E], G [auth H], H [auth I], I [auth F], K, L	486	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.273 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.32	α = 90
b = 121.76	β = 90
c = 234.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Nagarathinam, K., Krey, T.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	KR 2880 / 3-1

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release
  
• Version 1.1: 2025-04-30
  Changes: Database references