7KKL | pdb_00007kkl

SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6

• PDB DOI: https://doi.org/10.2210/pdb7KKL/pdb
• EM Map EMD-22910: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
• Expression System: Cricetulus griseus, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-10-27 Released: 2020-11-11 
• Deposition Author(s): Schoof, M.S., Faust, B.F., Saunders, R.A., Sangwan, S., Rezelj, V., Hoppe, N., Boone, M., Billesboelle, C.B., Puchades, C., Azumaya, C.M., Kratochvil, H.T., Zimanyi, M., Desphande, I., Liang, J., Dickinson, S., Nguyen, H.C., Chio, C.M., Merz, G.E., Thompson, M.C., Diwanji, D., Schaefer, K., Anand, A.A., Dobzinski, N., Zha, B.S., Simoneau, C.R., Leon, K., White, K.M., Chio, U.S., Gupta, M., Jin, M., Li, F., Liu, Y., Zhang, K., Bulkley, D., Sun, M., Smith, A.M., Rizo, A.N., Moss, F., Brilot, A.F., Pourmal, S., Trenker, R., Pospiech, T., Gupta, S., Barsi-Rhyne, B., Belyy, V., Barile-Hill, A.W., Nock, S., Liu, Y., Krogan, N.J., Ralston, C.Y., Swaney, D.L., Garcia-Sastre, A., Ott, M., Vignuzzi, M., Walter, P., Manglik, A., QCRG Structural Biology Consortium
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike.

Schoof, M., Faust, B., Saunders, R.A., Sangwan, S., Rezelj, V., Hoppe, N., Boone, M., Billesbolle, C.B., Puchades, C., Azumaya, C.M., Kratochvil, H.T., Zimanyi, M., Deshpande, I., Liang, J., Dickinson, S., Nguyen, H.C., Chio, C.M., Merz, G.E., Thompson, M.C., Diwanji, D., Schaefer, K., Anand, A.A., Dobzinski, N., Zha, B.S., Simoneau, C.R., Leon, K., White, K.M., Chio, U.S., Gupta, M., Jin, M., Li, F., Liu, Y., Zhang, K., Bulkley, D., Sun, M., Smith, A.M., Rizo, A.N., Moss, F., Brilot, A.F., Pourmal, S., Trenker, R., Pospiech, T., Gupta, S., Barsi-Rhyne, B., Belyy, V., Barile-Hill, A.W., Nock, S., Liu, Y., Krogan, N.J., Ralston, C.Y., Swaney, D.L., Garcia-Sastre, A., Ott, M., Vignuzzi, M., QCRG Structural Biology Consortium, Walter, P., Manglik, A.

(2020) Science 370: 1473-1479

• PubMed: 33154106 
• DOI: https://doi.org/10.1126/science.abe3255
• Primary Citation Related Structures: 
  7KKJ, 7KKK, 7KKL


• PubMed Abstract: 
  

  The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryo-electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia.

---

Organizational Affiliation: 
• Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA. [e-mail] [e-mail] [e-mail].
Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.
Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.
Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.
Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA, USA.
Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA.
Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France.
Department of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA.
Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
J. David Gladstone Institutes, San Francisco, CA, USA.
Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Molecular Biophysics and Integrated Bioimaging and the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Cytiva Life Sciences, Marlborough, MA, USA.
Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA. [e-mail] [e-mail] [e-mail].
Department of Anesthesia and Perioperative Care, University of California at San Francisco, San Francisco, CA, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 481.73 kDa 
• Atom Count: 27,024 
• Modeled Residue Count: 3,360 
• Deposited Residue Count: 4,239 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, C, E [auth D]	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
Glycosylation
Glycosylation Sites: 15		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic nanobody mNb6	B, D [auth E], F	125	synthetic construct	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	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	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], 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 D], RA [auth D], SA [auth D], TA [auth D], UA [auth D], VA [auth D], WA [auth D], XA [auth D], Y [auth A], YA [auth D], 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: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cisTEM	1.0.0
MODEL REFINEMENT	PHENIX	1.18.2-3874

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-11 
Deposition Author(s): Schoof, M.S., Faust, B.F., Saunders, R.A., Sangwan, S., Rezelj, V., Hoppe, N., Boone, M., Billesboelle, C.B., Puchades, C., Azumaya, C.M., Kratochvil, H.T., Zimanyi, M., Desphande, I., Liang, J., Dickinson, S., Nguyen, H.C., Chio, C.M., Merz, G.E., Thompson, M.C., Diwanji, D., Schaefer, K., Anand, A.A., Dobzinski, N., Zha, B.S., Simoneau, C.R., Leon, K., White, K.M., Chio, U.S., Gupta, M., Jin, M., Li, F., Liu, Y., Zhang, K., Bulkley, D., Sun, M., Smith, A.M., Rizo, A.N., Moss, F., Brilot, A.F., Pourmal, S., Trenker, R., Pospiech, T., Gupta, S., Barsi-Rhyne, B., Belyy, V., Barile-Hill, A.W., Nock, S., Liu, Y., Krogan, N.J., Ralston, C.Y., Swaney, D.L., Garcia-Sastre, A., Ott, M., Vignuzzi, M., Walter, P., Manglik, A., QCRG Structural Biology Consortium

---

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2020-11-11
  Type: Initial release
  
• Version 1.1: 2020-11-25
  Changes: Database references
• Version 1.2: 2020-12-30
  Changes: Database references
• Version 1.3: 2021-01-27
  Changes: Structure summary
• Version 1.4: 2021-04-21
  Changes: Database references
• Version 1.5: 2024-10-16
  Changes: Data collection, Database references, Refinement description, Structure summary