7KSG

SARS-CoV-2 spike in complex with nanobodies E

• PDB DOI:  https://doi.org/10.2210/pdb7KSG/pdb
• EM Map EMD-23018: EMDB EMDataResource

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


• Deposited: 2020-11-22 Released: 2021-01-20 
• Deposition Author(s): Hallberg, B.M., Das, H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.

Koenig, P.A., Das, H., Liu, H., Kummerer, B.M., Gohr, F.N., Jenster, L.M., Schiffelers, L.D.J., Tesfamariam, Y.M., Uchima, M., Wuerth, J.D., Gatterdam, K., Ruetalo, N., Christensen, M.H., Fandrey, C.I., Normann, S., Todtmann, J.M.P., Pritzl, S., Hanke, L., Boos, J., Yuan, M., Zhu, X., Schmid-Burgk, J.L., Kato, H., Schindler, M., Wilson, I.A., Geyer, M., Ludwig, K.U., Hallberg, B.M., Wu, N.C., Schmidt, F.I.

(2021) Science 371

• PubMed: 33436526 
• DOI: https://doi.org/10.1126/science.abe6230
• Primary Citation of Related Structures:  
  7B14, 7B17, 7B18, 7KN5, 7KN6, 7KN7, 7KSG


• PubMed Abstract: 
  

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost advantages over conventional antibodies. In this study, we generated four neutralizing nanobodies that target the receptor binding domain of the SARS-CoV-2 spike protein. We used x-ray crystallography and cryo-electron microscopy to define two distinct binding epitopes. On the basis of these structures, we engineered multivalent nanobodies with more than 100 times the neutralizing activity of monovalent nanobodies. Biparatopic nanobody fusions suppressed the emergence of escape mutants. Several nanobody constructs neutralized through receptor binding competition, whereas other monovalent and biparatopic nanobodies triggered aberrant activation of the spike fusion machinery. These premature conformational changes in the spike protein forestalled productive fusion and rendered the virions noninfectious.

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Organizational Affiliation: 

Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 485.3 kDa 
• Atom Count: 28,405 
• Modelled Residue Count: 3,558 
• Deposited Residue Count: 4,293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5  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
Nanobody against SARS-CoV-2 glycoprotein	D, E, F	143	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], 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 B], WA [auth C], X [auth B], XA [auth C], Y [auth B], YA [auth C], Z [auth B], 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: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.15

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Hallberg, B.M., Das, H.

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-06-30
  Changes: Data collection, Database references, Source and taxonomy, Structure summary