7TB8

Cryo-EM structure of SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1

• PDB DOI:  https://doi.org/10.2210/pdb7TB8/pdb
• EM Map EMD-25794: EMDB EMDataResource

• Classification: VIRAL PROTEIN/Immune System
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-12-21 Released: 2022-03-30 
• Deposition Author(s): Zhou, T., Tsybovsky, T., Kwong, P.D.
• 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: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529.

Zhou, T., Wang, L., Misasi, J., Pegu, A., Zhang, Y., Harris, D.R., Olia, A.S., Talana, C.A., Yang, E.S., Chen, M., Choe, M., Shi, W., Teng, I.T., Creanga, A., Jenkins, C., Leung, K., Liu, T., Stancofski, E.D., Stephens, T., Zhang, B., Tsybovsky, Y., Graham, B.S., Mascola, J.R., Sullivan, N.J., Kwong, P.D.

(2022) Science 376: eabn8897-eabn8897

• PubMed: 35324257 
• DOI: https://doi.org/10.1126/science.abn8897
• Primary Citation of Related Structures:  
  7TB8, 7TBF, 7TC9, 7TCA, 7TCC, 7U0D


• PubMed Abstract: 
  

The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo-electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)-binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies-including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404-that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants.

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Organizational Affiliation: 

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 11-mer - A3B3C3D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 11-mer - A8B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 508.04 kDa 
• Atom Count: 33,230 
• Modelled Residue Count: 4,189 
• Deposited Residue Count: 4,518 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,195	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
The heavy chain of SARS-CoV-2 antibody A19-61.1	D, F, J	127	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
The light chain of SARS-COV-2 antibody A19-61.1	E, G, K	107	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
The heavy chain of SARS-CoV-2 antiboddy antibody B1-182.1	H	123	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
The light chain of SARS-COV-2 antibody B1-182.1	I [auth L]	108	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth I], N, O, P, Q, R, S, T	2	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	2	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G79924RM GlyCosmos:  G79924RM GlyGen:  G79924RM

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth A], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [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: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.15
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Zhou, T., Tsybovsky, T., Kwong, P.D.

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

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 1.1: 2022-10-19
  Changes: Database references