Biological Assembly 1  

 3D View: Structure | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 478.15 kDa 
• Atom Count: 28286 
• Modelled Residue Count: 3510 
• Deposited Residue Count: 4206 
• Unique protein chains: 2

7A29

Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation

• DOI: 10.2210/pdb7A29/pdb
• EMDataResource: EMD-11617

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


• Deposited: 2020-08-16 Released: 2020-10-21 
• Deposition Author(s): Hallberg, B.M., Das, H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2.

Custodio, T.F., Das, H., Sheward, D.J., Hanke, L., Pazicky, S., Pieprzyk, J., Sorgenfrei, M., Schroer, M.A., Gruzinov, A.Y., Jeffries, C.M., Graewert, M.A., Svergun, D.I., Dobrev, N., Remans, K., Seeger, M.A., McInerney, G.M., Murrell, B., Hallberg, B.M., Low, C.

(2020) Nat Commun 11: 5588-5588

• PubMed: 33149112 
• DOI: 10.1038/s41467-020-19204-y
• Primary Citation of Related Structures:  
  7A25, 7A29


• PubMed Abstract: 
  

The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC ₅₀ of 0.6 µg/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed an unusual conformation of the spike where two RBDs are in the 'up' ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.

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Organizational Affiliation: 

Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1288	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
Neutralising sybody (Sb23)	D, E, F	114	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J, K, L, M, N	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], AB [auth C], BA [auth A], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], FB [auth C], GA [auth B], GB [auth C], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], 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: 2.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-08-16 
• Released Date: 2020-10-21 
Deposition Author(s): Hallberg, B.M., Das, H.

Revision History  

• Version 1.0: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2020-11-11
  Changes: Database references
• Version 1.2: 2020-11-18
  Changes: Database references