7CAI

SARS-CoV-2 S trimer with two RBDs in the open state and complexed with two H014 Fab

• PDB DOI:  https://doi.org/10.2210/pdb7CAI/pdb
• EM Map EMD-30332: EMDB EMDataResource

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


• Deposited: 2020-06-08 Released: 2020-09-23 
• Deposition Author(s): Zhe, L., Cao, L., Deng, Y., Sun, Y., Wang, N., Xie, L., Wang, Y., Rao, Z., Qin, C., Wang, X.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.49 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody.

Lv, Z., Deng, Y.Q., Ye, Q., Cao, L., Sun, C.Y., Fan, C., Huang, W., Sun, S., Sun, Y., Zhu, L., Chen, Q., Wang, N., Nie, J., Cui, Z., Zhu, D., Shaw, N., Li, X.F., Li, Q., Xie, L., Wang, Y., Rao, Z., Qin, C.F., Wang, X.

(2020) Science 369: 1505-1509

• PubMed: 32703908 
• DOI: https://doi.org/10.1126/science.abc5881
• Primary Citation of Related Structures:  
  7CAB, 7CAC, 7CAH, 7CAI, 7CAK


• PubMed Abstract: 
  

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in an unprecedented public health crisis. There are no approved vaccines or therapeutics for treating COVID-19. Here we report a humanized monoclonal antibody, H014, that efficiently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 at nanomolar concentrations by engaging the spike (S) receptor binding domain (RBD). H014 administration reduced SARS-CoV-2 titers in infected lungs and prevented pulmonary pathology in a human angiotensin-converting enzyme 2 mouse model. Cryo-electron microscopy characterization of the SARS-CoV-2 S trimer in complex with the H014 Fab fragment unveiled a previously uncharacterized conformational epitope, which was only accessible when the RBD was in an open conformation. Biochemical, cellular, virological, and structural studies demonstrated that H014 prevents attachment of SARS-CoV-2 to its host cell receptors. Epitope analysis of available neutralizing antibodies against SARS-CoV and SARS-CoV-2 uncovered broad cross-protective epitopes. Our results highlight a key role for antibody-based therapeutic interventions in the treatment of COVID-19.

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Organizational Affiliation: 

University of Chinese Academy of Sciences, Beijing 100049, China.

Biological Assembly 1  

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: 508.82 kDa 
• Atom Count: 31,266 
• Modelled Residue Count: 3,911 
• Deposited Residue Count: 4,490 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,208	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 8  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
Light chain of H014 Fab	D, F	210	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of H014 Fab	E, G	223	Homo sapiens	Mutation(s): 0

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	H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V	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 A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A], 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: 3.49 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Zhe, L., Cao, L., Deng, Y., Sun, Y., Wang, N., Xie, L., Wang, Y., Rao, Z., Qin, C., Wang, X.

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references