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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibodies CV07-287 and COVA1-16

X-ray diffraction
2.45Å resolution
PDB entry 7s5r coloured by chain, front view.
PDB entry 7s5r coloured by chain, side view.
PDB entry 7s5r coloured by chain, top view.
Source organisms:
Assembly composition:
hetero pentamer (preferred)
Entry contents: 5 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 and IG-heavy chain and IG-light kappa chain
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Multimeric state: hetero pentamer
Accessible surface area: 46126.87 Å2
Buried surface area: 13775.44 Å2
Dissociation area: 1,094.49 Å2
Dissociation energy (ΔGdiss): -0.77 kcal/mol
Dissociation entropy (TΔSdiss): 14.53 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-209916

Macromolecules

Spike protein S1
Chain: A
Length: 231 amino acids
Theoretical weight: 26.1 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P0DTC2 (Residues: 319-541; Coverage: 18%)
Gene names: 2, S
Pfam: Betacoronavirus spike glycoprotein S1, receptor binding
InterPro:
Spike protein S1 in PDB entry 7s5r, assembly 1, front view.
Spike protein S1 in PDB entry 7s5r, assembly 1, side view.
Spike protein S1 in PDB entry 7s5r, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P0DTC2  
123120406080100120140160180200220
 
100200RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFSGHHHHHH
UniProt
P0DTC2
Chains
Domains
Secondary structure
Ligand binding sites
Sequence conservation
Molecule details ›

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COVA1-16 Heavy chain
Chain: H
Length: 232 amino acids
Theoretical weight: 25.1 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
InterPro:
COVA1-16 Heavy chain in PDB entry 7s5r, assembly 1, front view.
COVA1-16 Heavy chain in PDB entry 7s5r, assembly 1, side view.
COVA1-16 Heavy chain in PDB entry 7s5r, assembly 1, top view.
123220406080100120140160180200220
 
100200QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYYMHWVRQAPGQGLEWMGIINSSGGSTSYAQKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARPPRNYYDRSGYYQRAEYFQHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC
Chains
RSRZ Outlier Chain B (auth H)
Chain B (auth H)
Domains
Secondary structure
Ligand binding sites
Sequence conservation
Molecule details ›

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COVA1-16 Light chain
Chain: L
Length: 214 amino acids
Theoretical weight: 23.42 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
InterPro:
COVA1-16 Light chain in PDB entry 7s5r, assembly 1, front view.
COVA1-16 Light chain in PDB entry 7s5r, assembly 1, side view.
COVA1-16 Light chain in PDB entry 7s5r, assembly 1, top view.
121420406080100120140160180200
 
100200DIQLTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQRPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNPPLTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Chains
RSRZ Outlier Chain C (auth L)
Chain C (auth L)
Domains
Secondary structure
Ligand binding sites
Sequence conservation
Molecule details ›

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CV07-287 Heavy chain
Chain: B
Length: 226 amino acids
Theoretical weight: 24.17 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
InterPro:
CV07-287 Heavy chain in PDB entry 7s5r, assembly 1, front view.
CV07-287 Heavy chain in PDB entry 7s5r, assembly 1, side view.
CV07-287 Heavy chain in PDB entry 7s5r, assembly 1, top view.
122620406080100120140160180200220
 
100200QVQLVQSGPEVKKPGTSVKVSCKASGFTFTSSAMQWVRQARGQRLEWIGWIVVGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSTNCYDAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
Chains
RSRZ Outlier Chain D (auth B)
Chain D (auth B)
Domains
Secondary structure
Ligand binding sites
Sequence conservation
Molecule details ›

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CV07-287 Light chain
Chain: C
Length: 216 amino acids
Theoretical weight: 23.53 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
InterPro:
CV07-287 Light chain in PDB entry 7s5r, assembly 1, front view.
CV07-287 Light chain in PDB entry 7s5r, assembly 1, side view.
CV07-287 Light chain in PDB entry 7s5r, assembly 1, top view.
121620406080100120140160180200
 
100200EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS
Chains
RSRZ Outlier Chain E (auth C)
Chain E (auth C)
Domains
Secondary structure
Ligand binding sites
Sequence conservation
Molecule details ›

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