› 7sn0

X-ray diffraction
3.08Å resolution

Crystal structure of spike protein receptor binding domain of escape mutant SARS-CoV-2 from immunocompromised patient (d146*) in complex with human receptor ACE2

Released:
DOI: 10.2210/pdb7sn0/pdb
PDB entry 7sn0 coloured by chain, front view.
PDB entry 7sn0 coloured by chain, side view.
PDB entry 7sn0 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.
Nabel KG, Clark SA, Shankar S, Pan J, Clark LE, Yang P, Coscia A, McKay LGA, Varnum HH, Brusic V, Tolan NV, Zhou G, Desjardins M, Turbett SE, Kanjilal S, Sherman AC, Dighe A, LaRocque RC, Ryan ET, Tylek C, Cohen-Solal JF, Darcy AT, Tavella D, Clabbers A, Fan Y, Griffiths A, Correia IR, Seagal J, Baden LR, Charles RC, Abraham J
OpenAccess logo Science 375 eabl6251 (2022)
PMID: 34855508

Function and Biology Details

Reaction catalysed: 
Angiotensin II + H(2)O = angiotensin-(1-7) + L-phenylalanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-144194 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (10 distinct):
Processed angiotensin-converting enzyme 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 621 amino acids
Theoretical weight: 71.83 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9BYF1 (Residues: 1-615; Coverage: 76%)
Gene names: ACE2, UNQ868/PRO1885
Sequence domains: Angiotensin-converting enzyme
Spike protein S1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 271 amino acids
Theoretical weight: 30.21 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 319-541; Coverage: 18%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, GAL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, GAL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, GAL
Carbohydrate polymer
3 bound ligands:
Ligand ZN 2 x ZN
Ligand CL 2 x CL
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 85.709Å b: 104.015Å c: 223.911Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.235 0.286
Expression system: Homo sapiens

Quick links

Citations

12 review citations

Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants.
Mittal et al. (2022)
11 more