› 8dls

Electron Microscopy
2.66Å resolution

Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8)

Released:
DOI: 10.2210/pdb8dls/pdb
PDB entry 8dls coloured by chain, front view.
PDB entry 8dls coloured by chain, side view.
PDB entry 8dls coloured by chain, top view.
Source organisms:
Primary publication:
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Mannar D, Saville JW, Sun Z, Zhu X, Marti MM, Srivastava SS, Berezuk AM, Zhou S, Tuttle KS, Sobolewski MD, Kim A, Treat BR, Da Silva Castanha PM, Jacobs JL, Barratt-Boyes SM, Mellors JW, Dimitrov DS, Li W, Subramaniam S
OpenAccess logo Nat Commun 13 4696 (2022)
PMID: 35982054
Related structures: EMD-27514

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-272881 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike glycoprotein Chain: A
Molecule details ›
Chain: A
Length: 1288 amino acids
Theoretical weight: 142.49 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 1-1208; Coverage: 95%)
Gene names: 2, S
Sequence domains:
Fab 4A8 heavy chain Chain: H
Molecule details ›
Chain: H
Length: 258 amino acids
Theoretical weight: 27.65 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Fab 4A8 light chain Chain: L

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 2.66Å
Relevant EMDB volumes: EMD-27514
Expression system: Homo sapiens

Quick links

Citations

5 review citations

Evolution of the SARS-CoV-2 Omicron spike.
Parsons et al. (2023)
4 more

2 mentions without citation

Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein.
Shikha et al. (2023)
1 more