7KKL

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 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.QCRG Structural Biology ConsortiumWalter, 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
Spike glycoproteinA,
C,
E [auth D]
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Synthetic nanobody mNb6B,
D [auth E],
F
125synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
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:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM1.0.0
MODEL REFINEMENTPHENIX1.18.2-3874

Structure Validation

View Full Validation Report



Entry History & Funding Information

Revision History  (Full details and data files)

  • 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