8TGV | pdb_00008tgv

CryoEM structure of Fab HC84.26-HCV E2 complex

• PDB DOI: https://doi.org/10.2210/pdb8TGV/pdb
• EM Map EMD-41245: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Orthohepacivirus hominis, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-07-13 Released: 2024-07-24 
• Deposition Author(s): Shahid, S., Liqun, J., LIu, Y., Hasan, S.S., Mariuzza, R.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 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 11-mer - A4B4C3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 11-mer - A6B3C2 Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A4B4 

Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 309.57 kDa 
• Atom Count: 16,520 
• Modeled Residue Count: 2,236 
• Deposited Residue Count: 2,829 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
envelope glycoprotein E2	A, D, G	291	Orthohepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for X4ZFZ7 (Hepatitis C virus genotype 1b) Explore X4ZFZ7  Go to UniProtKB:  X4ZFZ7
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HC84.26 Heavy chain	B [auth E], E [auth B], H [auth I], J [auth K]	255	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HC84.26 Light chain	C [auth F], F [auth C], I [auth J], K [auth L]	234	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth Z]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth H], N [auth M], O [auth N]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Shahid, S., Liqun, J., LIu, Y., Hasan, S.S., Mariuzza, R.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI168048

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.2: 2025-05-28
  Changes: Data collection
• Version 1.3: 2025-07-09
  Changes: Data collection, Database references