7OAN | pdb_00007oan

Nanobody C5 bound to Spike

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7OAN

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 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.

Macromolecule Content 

  • Total Structure Weight: 475.69 kDa 
  • Atom Count: 28,203 
  • Modeled Residue Count: 3,510 
  • Deposited Residue Count: 4,167 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,260Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S, 2
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: 17
Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
immunoglobulin mu heavy chainD [auth F],
E [auth G],
F [auth H]		129Vicugna pacosMutation(s): 0 
Gene Names: LOC102538064

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth C]
BA [auth A]
BB [auth C]
CA [auth A]
AA [auth A],
AB [auth C],
BA [auth A],
BB [auth C],
CA [auth A],
CB [auth C],
DA [auth A],
DB [auth C],
EA [auth A],
EB [auth C],
FA [auth A],
GA [auth A],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
OA [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth C],
UA [auth C],
V [auth A],
VA [auth C],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C],
Z [auth A],
ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

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: 2024-10-23
    Changes: Data collection, Refinement description, Structure summary