ISDA

Entry Detail

PDB ID:

7KKK

EMDB ID:

EMD-22907

Keywords:

VIRAL PROTEIN/IMMUNE SYSTEM

Title:

SARS-CoV-2 Spike in complex with neutralizing nanobody Nb6

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2, synthetic construct

Host Organism:

Cricetulus griseus

PDB Version:

Deposition Date:

2020-10-27

Release Date:

2020-11-11

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.03 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Spike glycoprotein
Chain IDs:A, C, E
Chain Length:1288
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF16451, PF09408, PF19209, PF01601

Polymer Type:polypeptide(L)
Description:Synthetic nanobody Nb6
Chain IDs:B, D, F
Chain Length:119
Number of Molecules:3
Biological Source:synthetic construct

Ligand Molecules

NAG

Primary Citation

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.Show

Science 370 1473 1479 (2020)

PMID: 33154106 DOI: 10.1126/science.abe3255

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures