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SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region

Electron Microscopy
3.91Å resolution
PDB entry 8zc5 coloured by chain, front view.
PDB entry 8zc5 coloured by chain, side view.
PDB entry 8zc5 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero hexamer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Spike protein S2' and IG-light lambda chain and IG-heavy chain
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Multimeric state: hetero hexamer
Accessible surface area: 37115.33 Å2
Buried surface area: 9146.91 Å2
Dissociation area: 2,415.65 Å2
Dissociation energy (ΔGdiss): -12.44 kcal/mol
Dissociation entropy (TΔSdiss): 38.48 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-272973

Macromolecules

Spike protein S1
Chains: A, B
Length: 196 amino acids
Theoretical weight: 22.12 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 332-527; Coverage: 16%)
Gene names: 2, S
Pfam: Betacoronavirus spike glycoprotein S1, receptor binding
Spike protein S1 in PDB entry 8zc5, assembly 1, front view.
Spike protein S1 in PDB entry 8zc5, assembly 1, side view.
Spike protein S1 in PDB entry 8zc5, assembly 1, top view.
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Light chain of D1F6 Fab
Chains: C, D
Length: 110 amino acids
Theoretical weight: 11.62 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Light chain of D1F6 Fab in PDB entry 8zc5, assembly 1, front view.
Light chain of D1F6 Fab in PDB entry 8zc5, assembly 1, side view.
Light chain of D1F6 Fab in PDB entry 8zc5, assembly 1, top view.
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Heavy chain of D1F6 Fab
Chains: E, F
Length: 127 amino acids
Theoretical weight: 14.18 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Heavy chain of D1F6 Fab in PDB entry 8zc5, assembly 1, front view.
Heavy chain of D1F6 Fab in PDB entry 8zc5, assembly 1, side view.
Heavy chain of D1F6 Fab in PDB entry 8zc5, assembly 1, top view.
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