› 7ydi

Electron Microscopy
3.98Å resolution

SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2, focused refinement of RBD region

Released:
DOI: 10.2210/pdb7ydi/pdb
PDB entry 7ydi coloured by chain, front view.
PDB entry 7ydi coloured by chain, side view.
PDB entry 7ydi coloured by chain, top view.
Source organisms:
Primary publication:
SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope.
He P, Liu B, Gao X, Yan Q, Pei R, Sun J, Chen Q, Hou R, Li Z, Zhang Y, Zhao J, Sun H, Feng B, Wang Q, Yi H, Hu P, Li P, Zhang Y, Chen Z, Niu X, Zhong X, Jin L, Liu X, Qu K, Ciazynska KA, Carter AP, Briggs JAG, Chen J, Liu J, Chen X, He J, Chen L, Xiong X
OpenAccess logo Nat Microbiol 7 1635-1649 (2022)
PMID: 36151403
Related structures: EMD-33748

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 tetramer (preferred)
PDBe Complex ID:
PDB-CPX-225166 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Processed angiotensin-converting enzyme 2 Chain: A
Molecule details ›
Chain: A
Length: 602 amino acids
Theoretical weight: 69.72 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9BYF1 (Residues: 19-615; Coverage: 76%)
Gene names: ACE2, UNQ868/PRO1885
Sequence domains: Angiotensin-converting enzyme
Spike protein S1 Chain: E
Molecule details ›
Chain: E
Length: 193 amino acids
Theoretical weight: 21.68 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 334-526; Coverage: 15%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Heavy chain of R1-32 Chain: H
Molecule details ›
Chain: H
Length: 228 amino acids
Theoretical weight: 23.84 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Light chain of R1-32 Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 22.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand NAG 4 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.98Å
Relevant EMDB volumes: EMD-33748
Expression system: Homo sapiens

Quick links

Citations

1 review citation

Overview of immunological & virological factors driving the evolution & global spread of SARS-CoV-2 variants.
Ramasamy R. (2023)
15 other articles