7KKJ

Structure of anti-SARS-CoV-2 Spike nanobody mNb6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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.Walter, P.Manglik, A.

(2020) Science 370: 1473-1479

  • DOI: https://doi.org/10.1126/science.abe3255
  • Primary Citation of 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

    Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synthetic nanobody mNb6A,
B [auth C]
125synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.569α = 90
b = 71.253β = 114.93
c = 46.43γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description