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SARS-CoV-2 Spike RBD in complex with neutralizing Fab 2H04 (local refinement)

Electron Microscopy
3.14Å resolution
PDB entry 7k9k coloured by chain, front view.
PDB entry 7k9k coloured by chain, side view.
PDB entry 7k9k 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: 18526.44 Å2
Buried surface area: 4425.51 Å2
Dissociation area: 1,820.89 Å2
Dissociation energy (ΔGdiss): -1.7 kcal/mol
Dissociation entropy (TΔSdiss): 23.23 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-534809

Macromolecules

Spike protein S1
Chain: A
Length: 195 amino acids
Theoretical weight: 21.87 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 333-527; Coverage: 16%)
Gene names: 2, S
Pfam: Betacoronavirus spike glycoprotein S1, receptor binding
InterPro:
Spike protein S1 in PDB entry 7k9k, assembly 1, front view.
Spike protein S1 in PDB entry 7k9k, assembly 1, side view.
Spike protein S1 in PDB entry 7k9k, assembly 1, top view.
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2H04 heavy chain
Chain: H
Length: 121 amino acids
Theoretical weight: 13.45 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
InterPro:
2H04 heavy chain in PDB entry 7k9k, assembly 1, front view.
2H04 heavy chain in PDB entry 7k9k, assembly 1, side view.
2H04 heavy chain in PDB entry 7k9k, assembly 1, top view.
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2H04 light chain
Chain: L
Length: 106 amino acids
Theoretical weight: 11.46 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
InterPro:
2H04 light chain in PDB entry 7k9k, assembly 1, front view.
2H04 light chain in PDB entry 7k9k, assembly 1, side view.
2H04 light chain in PDB entry 7k9k, assembly 1, top view.
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