8BEV | pdb_00008bev

Cryo-EM structure of SARS-CoV-2 spike (HexaPro variant) in complex with nanobody W25 (map 3, focus refinement on RBD, W25 and adjacent NTD)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8BEV

This is version 1.3 of the entry. See complete history

Literature

A nanobody recognizes a unique conserved epitope and potently neutralizes SARS-CoV-2 omicron variants.

Modhiran, N.Lauer, S.M.Amarilla, A.A.Hewins, P.Lopes van den Broek, S.I.Low, Y.S.Thakur, N.Liang, B.Nieto, G.V.Jung, J.Paramitha, D.Isaacs, A.Sng, J.D.J.Song, D.Jorgensen, J.T.Cheuquemilla, Y.Burger, J.Andersen, I.V.Himelreichs, J.Jara, R.MacLoughlin, R.Miranda-Chacon, Z.Chana-Cuevas, P.Kramer, V.Spahn, C.Mielke, T.Khromykh, A.A.Munro, T.Jones, M.L.Young, P.R.Chappell, K.Bailey, D.Kjaer, A.Herth, M.M.Jurado, K.A.Schwefel, D.Rojas-Fernandez, A.Watterson, D.

(2023) iScience 26: 107085-107085

  • DOI: https://doi.org/10.1016/j.isci.2023.107085
  • Primary Citation Related Structures: 
    8BEV, 8BGG

  • PubMed Abstract: 

    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) Omicron variant sub-lineages spread rapidly worldwide, mostly due to their immune-evasive properties. This has put a significant part of the population at risk for severe disease and underscores the need for effective anti-SARS-CoV-2 agents against emergent strains in vulnerable patients. Camelid nanobodies are attractive therapeutic candidates due to their high stability, ease of large-scale production, and potential for delivery via inhalation. Here, we characterize the receptor binding domain (RBD)-specific nanobody W25 and show superior neutralization activity toward Omicron sub-lineages in comparison to all other SARS-CoV2 variants. Structure analysis of W25 in complex with the SARS-CoV2 spike glycoprotein shows that W25 engages an RBD epitope not covered by any of the antibodies previously approved for emergency use. In vivo evaluation of W25 prophylactic and therapeutic treatments across multiple SARS-CoV-2 variant infection models, together with W25 biodistribution analysis in mice, demonstrates favorable pre-clinical properties. Together, these data endorse W25 for further clinical development.


  • Organizational Affiliation
    • School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia.

Macromolecule Content 

  • Total Structure Weight: 301.31 kDa 
  • Atom Count: 4,483 
  • Modeled Residue Count: 542 
  • Deposited Residue Count: 2,701 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, C
1,267Severe 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: 4Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
immunoglobulin mu heavy chain167Vicugna pacosMutation(s): 0 
Gene Names: LOC102538064

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth E],
E [auth F],
F [auth G]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth H]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
H [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: 5.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySCHW 1851/1-2

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-09
    Changes: Data collection
  • Version 1.3: 2025-07-16
    Changes: Data collection, Database references