› 7xcp

Electron Microscopy
3.05Å resolution

Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 Fab

Released:
DOI: 10.2210/pdb7xcp/pdb
PDB entry 7xcp coloured by chain, front view.
PDB entry 7xcp coloured by chain, side view.
PDB entry 7xcp coloured by chain, top view.
Source organisms:
Primary publication:
Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
Nat Commun 13 4958-4958 (2022)
Related structures: EMD-33125

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-225165 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Processed angiotensin-converting enzyme 2 Chain: A
Molecule details ›
Chain: A
Length: 596 amino acids
Theoretical weight: 69.04 KDa
Source organism: Homo sapiens
Expression system: Mammalian expression vector EGFP-MCS-pcDNA3.1
UniProt:
  • Canonical: Q9BYF1 (Residues: 19-614; Coverage: 76%)
Gene names: ACE2, UNQ868/PRO1885
Sequence domains: Angiotensin-converting enzyme
Spike protein S1 Chain: B
Molecule details ›
Chain: B
Length: 195 amino acids
Theoretical weight: 22.17 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Mammalian expression vector EGFP-MCS-pcDNA3.1
UniProt:
  • Canonical: P0DTC2 (Residues: 333-527; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Heavy chain of 304 Fab Chain: H
Molecule details ›
Chain: H
Length: 223 amino acids
Theoretical weight: 23.73 KDa
Source organism: Homo sapiens
Expression system: Mammalian expression vector EGFP-MCS-pcDNA3.1
Lignt chain of 304 Fab Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.37 KDa
Source organism: Homo sapiens
Expression system: Mammalian expression vector EGFP-MCS-pcDNA3.1

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 5 x NAG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.05Å
Relevant EMDB volumes: EMD-33125
Expression system: Mammalian expression vector EGFP-MCS-pcDNA3.1

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