8Q95 | pdb_00008q95

Crystal structure of the SARS-CoV-2 BA.1 RBD with neutralizing-VHHs Ma16B06 and Ma3F05


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8Q95

This is version 1.2 of the entry. See complete history

Literature

Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.

Aksu, M.Kumar, P.Guttler, T.Taxer, W.Gregor, K.Mussil, B.Rymarenko, O.Stegmann, K.M.Dickmanns, A.Gerber, S.Reineking, W.Schulz, C.Henneck, T.Mohamed, A.Pohlmann, G.Ramazanoglu, M.Mese, K.Gross, U.Ben-Yedidia, T.Ovadia, O.Fischer, D.W.Kamensky, M.Reichman, A.Baumgartner, W.von Kockritz-Blickwede, M.Dobbelstein, M.Gorlich, D.

(2023) Antiviral Res 221: 105778-105778

  • DOI: https://doi.org/10.1016/j.antiviral.2023.105778
  • Primary Citation Related Structures: 
    8Q7S, 8Q93, 8Q94, 8Q95

  • PubMed Abstract: 

    The ongoing threat of COVID-19 has highlighted the need for effective prophylaxis and convenient therapies, especially for outpatient settings. We have previously developed highly potent single-domain (VHH) antibodies, also known as nanobodies, that target the Receptor Binding Domain (RBD) of the SARS-CoV-2 Spike protein and neutralize the Wuhan strain of the virus. In this study, we present a new generation of anti-RBD nanobodies with superior properties. The primary representative of this group, Re32D03, neutralizes Alpha to Delta as well as Omicron BA.2.75; other members neutralize, in addition, Omicron BA.1, BA.2, BA.4/5, and XBB.1. Crystal structures of RBD-nanobody complexes reveal how ACE2-binding is blocked and also explain the nanobodies' tolerance to immune escape mutations. Through the cryo-EM structure of the Ma16B06-BA.1 Spike complex, we demonstrated how a single nanobody molecule can neutralize a trimeric spike. We also describe a method for large-scale production of these nanobodies in Pichia pastoris, and for formulating them into aerosols. Exposing hamsters to these aerosols, before or even 24 h after infection with SARS-CoV-2, significantly reduced virus load, weight loss and pathogenicity. These results show the potential of aerosolized nanobodies for prophylaxis and therapy of coronavirus infections.


  • Organizational Affiliation
    • Max Planck Institute for Multidisciplinary Sciences, Dept. of Cellular Logistics, Am Fassberg 11, 37077 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 48.82 kDa 
  • Atom Count: 3,714 
  • Modeled Residue Count: 427 
  • Deposited Residue Count: 438 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1187Severe acute respiratory syndrome coronavirus 2Mutation(s): 15 
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody Ma3F05131Vicugna pacosMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody Ma16B06120Vicugna pacosMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.222α = 90
b = 89.56β = 111.63
c = 72.198γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary