8F5I | pdb_00008f5i

SARS-CoV-2 S2 helix epitope scaffold bound by antibody DH1057.1

• PDB DOI: https://doi.org/10.2210/pdb8F5I/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Rhodopseudomonas palustris, Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2022-11-14 Released: 2023-10-11 
• Deposition Author(s): Kapingidza, A.B., Wrapp, D., Winters, K., Azoitei, M.L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.244 (Depositor) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Engineered immunogens to elicit antibodies against conserved coronavirus epitopes.

Kapingidza, A.B., Marston, D.J., Harris, C., Wrapp, D., Winters, K., Mielke, D., Xiaozhi, L., Yin, Q., Foulger, A., Parks, R., Barr, M., Newman, A., Schafer, A., Eaton, A., Flores, J.M., Harner, A., Catanzaro Jr., N.J., Mallory, M.L., Mattocks, M.D., Beverly, C., Rhodes, B., Mansouri, K., Van Itallie, E., Vure, P., Dunn, B., Keyes, T., Stanfield-Oakley, S., Woods, C.W., Petzold, E.A., Walter, E.B., Wiehe, K., Edwards, R.J., Montefiori, D.C., Ferrari, G., Baric, R., Cain, D.W., Saunders, K.O., Haynes, B.F., Azoitei, M.L.

(2023) Nat Commun 14: 7897-7897

• PubMed: 38036525 
• DOI: https://doi.org/10.1038/s41467-023-43638-9
• Primary Citation Related Structures: 
  8F5H, 8F5I, 8FDO


• PubMed Abstract: 
  

  Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employ computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant receptor binding domain. These engineered proteins bind with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interact with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicit sera with broad betacoronavirus reactivity and protect as "boosts" against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.

---

Organizational Affiliation: 
• Duke Human Vaccine Institute, Duke University, Durham, NC, USA.
Department of Medicine, Duke University, Durham, NC, USA.
Department of Surgery, Duke University, Durham, NC, USA.
Center for Human Systems Immunology, Duke University, Durham, NC, USA.
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Center for Infectious Diseases and Diagnostic Innovation, Duke University Medical Center, Durham, NC, USA.
Department of Pediatrics, Duke University, Durham, NC, USA.
Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
Department of Immunology, Duke University, Durham, NC, USA.
Duke Human Vaccine Institute, Duke University, Durham, NC, USA. [e-mail].
Department of Medicine, Duke University, Durham, NC, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 119.81 kDa 
• Atom Count: 9,467 
• Modeled Residue Count: 1,050 
• Deposited Residue Count: 1,088 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Specialized acyl carrier protein	A, B	101	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: RPA2022
UniProt
Find proteins for Q6N882 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N882  Go to UniProtKB:  Q6N882

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1057.1 HC	C [auth H], E [auth X]	227	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1057.1 LC	D [auth L], F [auth Y]	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth I]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.244 (Depositor) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.68	α = 71.6
b = 76.36	β = 69.99
c = 79.02	γ = 88.3

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Kapingidza, A.B., Wrapp, D., Winters, K., Azoitei, M.L.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1P01AI158571-01A1

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Structure summary
• Version 1.3: 2026-03-04
  Changes: Refinement description