› 9css

Electron Microscopy
2.72Å resolution

Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, 1UP RBD conformation

Released:
DOI: 10.2210/pdb9css/pdb
PDB entry 9css coloured by chain, front view.
PDB entry 9css coloured by chain, side view.
PDB entry 9css coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Primary publication:
Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
Singh S, Liu Y, Burke M, Rayaprolu V, Stein SE, Hasan SS
J Struct Biol X 11 100123 (2025)
PMID: 40046771
Related structures: EMD-45893

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-144650 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (5 distinct):
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1275 amino acids
Theoretical weight: 140.68 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 19-1208; Coverage: 94%)
Gene names: 2, S
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
1 bound ligand:
Ligand NAG 24 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 2.72Å
Relevant EMDB volumes: EMD-45893
Expression system: Homo sapiens

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