› 7y9n

X-ray diffraction
1.88Å resolution

an engineered 5-helix bundle derived from SARS-CoV-2 S2 in complex with HR2P

Released:
DOI: 10.2210/pdb7y9n/pdb
PDB entry 7y9n coloured by chain, front view.
PDB entry 7y9n coloured by chain, side view.
PDB entry 7y9n coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Primary publication:
An engineered 5-helix bundle derived from SARS-CoV-2 S2 pre-binds sarbecoviral spike at both serological- and endosomal-pH to inhibit virus entry.
Lin X, Guo L, Lin S, Chen Z, Yang F, Yang J, Wang L, Wen A, Duan Y, Zhang X, Dai Y, Yin K, Yuan X, Yu C, He B, Cao Y, Dong H, Li J, Zhao Q, Lu G
OpenAccess logo Emerg Microbes Infect 11 1920-1935 (2022)
PMID: 35757908

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-534658 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Spike protein S2' Chain: A
Molecule details ›
Chain: A
Length: 250 amino acids
Theoretical weight: 26.35 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P0DTC2 (Residues: 917-1204; Coverage: 15%)
Gene names: 2, S
Sequence domains: Coronavirus spike glycoprotein S2
Spike protein S2' Chain: B
Molecule details ›
Chain: B
Length: 36 amino acids
Theoretical weight: 4.01 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 1168-1203; Coverage: 3%)
Gene names: 2, S

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 69.977Å b: 40.495Å c: 88.014Å
α: 90° β: 105.31° γ: 90°
R-values:
R R work R free
0.201 0.2 0.212
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

2 review citations

Clinical development of antivirals against SARS-CoV-2 and its variants.
Lan et al. (2024)
1 more