8HHY

SARS-CoV-2 Delta Spike in complex with IS-9A

• PDB DOI:  https://doi.org/10.2210/pdb8HHY/pdb
• EM Map EMD-34807: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-11-17 Released: 2023-02-01 
• Deposition Author(s): Mohapatra, A., Wu, Y.-M.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.

Huang, K.A., Chen, X., Mohapatra, A., Nguyen, H.T.V., Schimanski, L., Tan, T.K., Rijal, P., Vester, S.K., Hills, R.A., Howarth, M., Keeffe, J.R., Cohen, A.A., Kakutani, L.M., Wu, Y.M., Shahed-Al-Mahmud, M., Chou, Y.C., Bjorkman, P.J., Townsend, A.R., Ma, C.

(2023) Nat Commun 14: 311-311

• PubMed: 36658148 
• DOI: https://doi.org/10.1038/s41467-023-35949-8
• Primary Citation of Related Structures:  
  7YCK, 7YCL, 7YCN, 8HHX, 8HHY, 8HHZ


• PubMed Abstract: 
  

Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.

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Organizational Affiliation: 

Genomics Research Center, Academia Sinica, Taipei, Taiwan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A3B3C2D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A5B3C1 Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Homo 3-mer - B3 

Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Homo 3-mer - B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 568.16 kDa 
• Atom Count: 27,420 
• Modelled Residue Count: 3,483 
• Deposited Residue Count: 5,094 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IS-9A Fab heavy chain	A [auth F], C [auth G], E [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IS-9A Fab light chain	B [auth W], D [auth I], F [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	G [auth A], H [auth B], I [auth C]	1,259	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 13  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth D], K [auth E], L [auth J], M [auth K]	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 (Subject of Investigation/LOI)	AA [auth B], BA [auth B], CA [auth B], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Mohapatra, A., Wu, Y.-M.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release