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Crystal structure of MERS-CoV spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC68.109 isolated from a vaccinated COVID-19 convalescent

X-ray diffraction
2.89Å resolution
PDB entry 8dgx coloured by chain, front view.
PDB entry 8dgx coloured by chain, side view.
PDB entry 8dgx coloured by chain, top view.
Source organisms:
Assembly composition:
hetero trimer (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-heavy chain and IG-light kappa chain
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Multimeric state: hetero trimer
Accessible surface area: 19461.57 Å2
Buried surface area: 4570.92 Å2
Dissociation area: 645.45 Å2
Dissociation energy (ΔGdiss): 2.96 kcal/mol
Dissociation entropy (TΔSdiss): 8.07 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-271375
Assembly 2
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Assembly Name: Spike protein S2' and IG-heavy chain and IG-light kappa chain
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Multimeric state: hetero trimer
Accessible surface area: 18888.78 Å2
Buried surface area: 4712.81 Å2
Dissociation area: 626.46 Å2
Dissociation energy (ΔGdiss): 3.73 kcal/mol
Dissociation entropy (TΔSdiss): 8.1 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-271375

Macromolecules

Antibody CC68.109 Fab heavy chain
Chains: A, H
Length: 221 amino acids
Theoretical weight: 23.61 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
Antibody CC68.109 Fab heavy chain in PDB entry 8dgx, assembly 1, front view.
Antibody CC68.109 Fab heavy chain in PDB entry 8dgx, assembly 1, side view.
Antibody CC68.109 Fab heavy chain in PDB entry 8dgx, assembly 1, top view.
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Antibody CC68.109 Fab light chain
Chains: B, L
Length: 218 amino acids
Theoretical weight: 23.87 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
Antibody CC68.109 Fab light chain in PDB entry 8dgx, assembly 1, front view.
Antibody CC68.109 Fab light chain in PDB entry 8dgx, assembly 1, side view.
Antibody CC68.109 Fab light chain in PDB entry 8dgx, assembly 1, top view.
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Spike protein S2'
Chains: C, D
Length: 27 amino acids
Theoretical weight: 2.99 KDa
Source organism: Betacoronavirus England 1
Expression system: Not provided
UniProt:
  • Canonical: K9N5Q8 (Residues: 1221-1247; Coverage: 2%)
Gene names: 3, S
Spike protein S2' in PDB entry 8dgx, assembly 1, front view.
Spike protein S2' in PDB entry 8dgx, assembly 1, side view.
Spike protein S2' in PDB entry 8dgx, assembly 1, top view.
PDBe-KB: UniProt Coverage View: K9N5Q8  
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