› 8bon

Electron Microscopy
3.2Å resolution

Structure of the SARS-CoV-2 spike glycoprotein in complex with the macrocyclic peptide S1B3inL1

Released:
DOI: 10.2210/pdb8bon/pdb
PDB entry 8bon coloured by chain, front view.
PDB entry 8bon coloured by chain, side view.
PDB entry 8bon coloured by chain, top view.
Source organisms:
Primary publication:
A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein.
Thijssen V, Hurdiss DL, Debski-Antoniak OJ, Spence MA, Franck C, Norman A, Aggarwal A, Mokiem NJ, van Dongen DAA, Vermeir SW, Liu M, Li W, Chatziandreou M, Donselaar T, Du W, Drulyte I, Bosch BJ, Snijder J, Turville SG, Payne RJ, Jackson CJ, van Kuppeveld FJM, Jongkees SAK
Proc Natl Acad Sci U S A 120 e2303292120 (2023)
PMID: 37339194
Related structures: EMD-16144

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219282 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Fibritin; Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1275 amino acids
Theoretical weight: 141.05 KDa
Source organisms: Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 14-1208; Coverage: 95%)
  • Canonical: P10104 (Residues: 458-484; Coverage: 6%)
Gene names: 2, S, wac
Sequence domains:
Macrocyclic peptide S1B3inL1 Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 19 amino acids
Theoretical weight: 2.25 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 23 x NAG
1 modified residue:
Ligand CCS 3 x CCS

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-16144
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

3 citation in other articles

A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein.
Thijssen et al. (2023)
2 more