Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 588.24 kDa 
• Atom Count: 31016 
• Modelled Residue Count: 3868 
• Deposited Residue Count: 5181 
• Unique protein chains: 3

7CZQ

S protein of SARS-CoV-2 in complex bound with P2B-1A10

• PDB DOI: 10.2210/pdb7CZQ/pdb
• EM Map EMD-30513: EMDB EMDataResource

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


• Deposited: 2020-09-09 Released: 2021-03-10 
• Deposition Author(s): Yan, R.H., Zhang, Y.Y., Li, Y.N., Zhou, Q.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies.

Yan, R., Wang, R., Ju, B., Yu, J., Zhang, Y., Liu, N., Wang, J., Zhang, Q., Chen, P., Zhou, B., Li, Y., Shen, Y., Zhang, S., Tian, L., Guo, Y., Xia, L., Zhong, X., Cheng, L., Ge, X., Zhao, J., Wang, H.W., Wang, X., Zhang, Z., Zhang, L., Zhou, Q.

(2021) Cell Res 31: 517-525

• PubMed: 33731853 
• DOI: 10.1038/s41422-021-00487-9
• Primary Citation of Related Structures:  
  7CZP, 7CZQ, 7CZR, 7CZS, 7CZT, 7CZU, 7CZV, 7CZW, 7CZX, 7CZY, 7CZZ, 7D00, 7D03, 7D0B, 7D0C, 7D0D


• PubMed Abstract: 
  

Neutralizing monoclonal antibodies (nAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent promising candidates for clinical intervention against coronavirus disease 2019 (COVID-19). We isolated a large number of nAbs from SARS-CoV-2-infected individuals capable of disrupting proper interaction between the receptor binding domain (RBD) of the viral spike (S) protein and the receptor angiotensin converting enzyme 2 (ACE2). However, the structural basis for their potent neutralizing activity remains unclear. Here, we report cryo-EM structures of the ten most potent nAbs in their native full-length IgG-form or in both IgG-form and Fab-form bound to the trimeric S protein of SARS-CoV-2. The bivalent binding of the full-length IgG is found to associate with more RBDs in the "up" conformation than the monovalent binding of Fab, perhaps contributing to the enhanced neutralizing activity of IgG and triggering more shedding of the S1 subunit from the S protein. Comparison of a large number of nAbs identified common and unique structural features associated with their potent neutralizing activities. This work provides a structural basis for further understanding the mechanism of nAbs, especially through revealing the bivalent binding and its correlation with more potent neutralization and the shedding of S1 subunit.

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Organizational Affiliation: 

Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1283	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
IG c642_heavy_IGHV3-53_IGHD1-26_IGHJ6,Chain H of P2B-1A10,Immunoglobulin gamma-1 heavy chain	D [auth H], F [auth J]	451	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5
Find proteins for A0A5C2GF00 (Homo sapiens) Explore A0A5C2GF00  Go to UniProtKB:  A0A5C2GF00
UniProt Groups	A0A5C2GF00P0DOX5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin kappa variable 1-33,Uncharacterized protein	E [auth K], G [auth N]	215	Homo sapiens	Mutation(s): 0  Gene Names: IGKV1-33
UniProt
Find proteins for P01594 (Homo sapiens) Explore P01594  Go to UniProtKB:  P01594
Find proteins for Q8TCD0 (Homo sapiens) Explore Q8TCD0  Go to UniProtKB:  Q8TCD0
UniProt Groups	Q8TCD0P01594

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	AA [auth a], BA [auth b], H [auth D], I [auth E], J [auth F], K [auth G], L [auth I], M [auth L], N [auth M], O, P, Q, R, S, T, U, V, W, X, Y, Z	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)	AB [auth C], BB [auth C], CA [auth A], CB [auth C], DA [auth A], DB [auth C], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-09-09 
• Released Date: 2021-03-10 
Deposition Author(s): Yan, R.H., Zhang, Y.Y., Li, Y.N., Zhou, Q.

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2021-05-05
  Changes: Database references
• Version 1.2: 2021-05-19
  Changes: Database references