6ZH9

Ternary complex CR3022 H11-H4 and RBD (SARS-CoV-2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2.

Huo, J.Le Bas, A.Ruza, R.R.Duyvesteyn, H.M.E.Mikolajek, H.Malinauskas, T.Tan, T.K.Rijal, P.Dumoux, M.Ward, P.N.Ren, J.Zhou, D.Harrison, P.J.Weckener, M.Clare, D.K.Vogirala, V.K.Radecke, J.Moynie, L.Zhao, Y.Gilbert-Jaramillo, J.Knight, M.L.Tree, J.A.Buttigieg, K.R.Coombes, N.Elmore, M.J.Carroll, M.W.Carrique, L.Shah, P.N.M.James, W.Townsend, A.R.Stuart, D.I.Owens, R.J.Naismith, J.H.

(2020) Nat Struct Mol Biol 27: 846-854

  • DOI: 10.1038/s41594-020-0469-6
  • Primary Citation of Related Structures:  
    6ZH9

  • PubMed Abstract: 
  • The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than influenza. The SARS-CoV-2 receptor binding domain (RBD) of the spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) recep ...

    The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than influenza. The SARS-CoV-2 receptor binding domain (RBD) of the spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor as a prelude to viral entry into the cell. Using a naive llama single-domain antibody library and PCR-based maturation, we have produced two closely related nanobodies, H11-D4 and H11-H4, that bind RBD (K D of 39 and 12 nM, respectively) and block its interaction with ACE2. Single-particle cryo-EM revealed that both nanobodies bind to all three RBDs in the spike trimer. Crystal structures of each nanobody-RBD complex revealed how both nanobodies recognize the same epitope, which partly overlaps with the ACE2 binding surface, explaining the blocking of the RBD-ACE2 interaction. Nanobody-Fc fusions showed neutralizing activity against SARS-CoV-2 (4-6 nM for H11-H4, 18 nM for H11-D4) and additive neutralization with the SARS-CoV-1/2 antibody CR3022.


    Organizational Affiliation

    Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK. naismith@strubi.ox.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CR3022 heavyHHH216Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CR3022 Light chainLLL219Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinEEE197Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody H11-H4FFF134Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.261 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.411α = 90
b = 156.411β = 90
c = 116.205γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom100209/Z/12/Z).
Engineering and Physical Sciences Research CouncilUnited KingdomRFI

Revision History 

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references