8TFE | pdb_00008tfe

Crystal structure of Fab fragment of anti-HCV E2 antibody (CBH-7)

• PDB DOI: https://doi.org/10.2210/pdb8TFE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-07-10 Released: 2024-07-17 
• Deposition Author(s): Shahid, S., Mariuzza, R.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Cryo-EM structures of HCV E2 glycoprotein bound to neutralizing and non-neutralizing antibodies determined using bivalent Fabs as fiducial markers.

Shahid, S., Karade, S.S., Hasan, S.S., Yin, R., Jiang, L., Liu, Y., Felbinger, N., Kulakova, L., Toth, E.A., Keck, Z.Y., Foung, S.K.H., Fuerst, T.R., Pierce, B.G., Mariuzza, R.A.

(2025) Commun Biol 8: 825-825

• PubMed: 40442315 
• DOI: https://doi.org/10.1038/s42003-025-08239-w
• Primary Citation of Related Structures:  
  8TFE, 8TGV, 8TGZ, 8THZ, 8TXQ, 8TZY, 8U9Y


• PubMed Abstract: 
  

  Global elimination of hepatitis C virus (HCV) will require an effective cross-genotype vaccine. The HCV E2 envelope glycoprotein is the main target of neutralizing antibodies but also contains epitopes that elicit non-neutralizing antibodies which may provide protection through Fc effector functions rather than direct neutralization. We determined cryo-EM structures of a broadly neutralizing antibody, a moderately neutralizing antibody, and a non-neutralizing antibody bound to E2 to resolutions of 3.8, 3.3, and 3.7 Å, respectively. Whereas the broadly neutralizing antibody targeted the front layer of E2 and the non-neutralizing antibody targeted the back layer, the moderately neutralizing antibody straddled both front and back layers, and thereby defined a new neutralizing epitope on E2. The small size of complexes between conventional (monovalent) Fabs and E2 (~110 kDa) presented a challenge for cryo-EM. Accordingly, we engineered bivalent versions of E2-specific Fabs that doubled the size of Fab-E2 complexes and conferred highly identifiable shapes to the complexes that facilitated particle selection and orientation for image processing. This study validates bivalent Fabs as new fiducial markers for cryo-EM analysis of small proteins such as HCV E2 and identifies a new target epitope for vaccine development.

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Organizational Affiliation: 
• W.M. Keck Laboratory for Structural Biology, University of Maryland-Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA.
Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Rockville, MD, USA.
Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA.
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
W.M. Keck Laboratory for Structural Biology, University of Maryland-Institute for Bioscience and Biotechnology Research, Rockville, MD, USA. [e-mail].
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 106.23 kDa 
• Atom Count: 7,329 
• Modeled Residue Count: 866 
• Deposited Residue Count: 978 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBH-7 Heavy chain	A, C	254	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CBH-7 Light chain	B, D	235	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC (Subject of Investigation/LOI)	H [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
EDO (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], I [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.935	α = 90
b = 101.912	β = 100.24
c = 109.936	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Shahid, S., Mariuzza, R.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 AI132213

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary
• Version 1.2: 2025-07-09
  Changes: Database references