7OAO

Nanobody C5 bound to RBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.152 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19.

Huo, J.Mikolajek, H.Le Bas, A.Clark, J.J.Sharma, P.Kipar, A.Dormon, J.Norman, C.Weckener, M.Clare, D.K.Harrison, P.J.Tree, J.A.Buttigieg, K.R.Salguero, F.J.Watson, R.Knott, D.Carnell, O.Ngabo, D.Elmore, M.J.Fotheringham, S.Harding, A.Moynie, L.Ward, P.N.Dumoux, M.Prince, T.Hall, Y.Hiscox, J.A.Owen, A.James, W.Carroll, M.W.Stewart, J.P.Naismith, J.H.Owens, R.J.

(2021) Nat Commun 12: 5469-5469

  • DOI: https://doi.org/10.1038/s41467-021-25480-z
  • Primary Citation of Related Structures:  
    7OAN, 7OAO, 7OAP, 7OAQ, 7OAU, 7OAY

  • PubMed Abstract: 

    SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain antibodies (nanobodies) have significant potential. Their small size and stability mean that nanobodies are compatible with respiratory administration. We report four nanobodies (C5, H3, C1, F2) engineered as homotrimers with pmolar affinity for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Crystal structures show C5 and H3 overlap the ACE2 epitope, whilst C1 and F2 bind to a different epitope. Cryo Electron Microscopy shows C5 binding results in an all down arrangement of the Spike protein. C1, H3 and C5 all neutralize the Victoria strain, and the highly transmissible Alpha (B.1.1.7 first identified in Kent, UK) strain and C1 also neutralizes the Beta (B.1.35, first identified in South Africa). Administration of C5-trimer via the respiratory route showed potent therapeutic efficacy in the Syrian hamster model of COVID-19 and separately, effective prophylaxis. The molecule was similarly potent by intraperitoneal injection.


  • Organizational Affiliation

    Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1A [auth EEE]210Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C5 nanobodyB [auth FFF]128Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth EEE]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth EEE]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.152 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.22α = 90
b = 154.33β = 90
c = 28.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom100209/Z/12/Z)
Engineering and Physical Sciences Research CouncilUnited KingdomEP/S025243/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description