› 8dw3

Electron Microscopy
4.26Å resolution

Cryo-EM structure of SARS-CoV-2 RBD in complex with anti-SARS-CoV-2 DARPin,SR16m, and two antibody Fabs, S309 and CR3022

Released:
DOI: 10.2210/pdb8dw3/pdb
PDB entry 8dw3 coloured by chain, front view.
PDB entry 8dw3 coloured by chain, side view.
PDB entry 8dw3 coloured by chain, top view.
Source organisms:
Primary publication:
A potent and broad neutralization of SARS-CoV-2 variants of concern by DARPins.
Chonira V, Kwon YD, Gorman J, Case JB, Ku Z, Simeon R, Casner RG, Harris DR, Olia AS, Stephens T, Shapiro L, Bender MF, Boyd H, Teng IT, Tsybovsky Y, Krammer F, Zhang N, Diamond MS, Kwong PD, An Z, Chen Z
Nat Chem Biol (2022)
PMID: 36411391
Related structures: EMD-27750

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-534690 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (7 distinct):
Anti-SARS-CoV-2 DARPin SR16m Chain: A
Molecule details ›
Chain: A
Length: 161 amino acids
Theoretical weight: 16.79 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Spike protein S1 Chain: B
Molecule details ›
Chain: B
Length: 197 amino acids
Theoretical weight: 22.1 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 330-526; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Antibody S309 light chain Chain: C
Molecule details ›
Chain: C
Length: 214 amino acids
Theoretical weight: 23.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
antibody S309 heavy chain Chain: D
Molecule details ›
Chain: D
Length: 230 amino acids
Theoretical weight: 24.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
antibody CR3022 heavy chain Chain: H
Molecule details ›
Chain: H
Length: 221 amino acids
Theoretical weight: 23.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
antibody CR3022 light chain Chain: L
Molecule details ›
Chain: L
Length: 220 amino acids
Theoretical weight: 24.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.26Å
Relevant EMDB volumes: EMD-27750
Expression system: Homo sapiens

Quick links

Citations

3 review citations

Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics.
Gupta et al. (2023)
2 more