› 7xsb

X-ray diffraction
3.2Å resolution

Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab

Released:
DOI: 10.2210/pdb7xsb/pdb
PDB entry 7xsb coloured by chain, front view.
PDB entry 7xsb coloured by chain, side view.
PDB entry 7xsb coloured by chain, top view.
Source organisms:
Primary publication:
Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Ju B, Zhang Q, Wang Z, Aw ZQ, Chen P, Zhou B, Wang R, Ge X, Lv Q, Cheng L, Zhang R, Wong YH, Chen H, Wang H, Shan S, Liao X, Shi X, Liu L, Chu JJH, Wang X, Zhang Z, Zhang L
OpenAccess logo Nat Immunol 24 690-699 (2023)
PMID: 36914890

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-225266 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chains: A, B, C, E
Molecule details ›
Chains: A, B, C, E
Length: 243 amino acids
Theoretical weight: 27.23 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P0DTC2 (Residues: 333-528; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
P5S-3B11 Heavy chain Chains: D, G, H, J
Molecule details ›
Chains: D, G, H, J
Length: 217 amino acids
Theoretical weight: 23.31 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
P5S-3B11 Light chain Chains: F, I, K, L
Molecule details ›
Chains: F, I, K, L
Length: 216 amino acids
Theoretical weight: 23.19 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P21
Unit cell:
a: 127.766Å b: 85.732Å c: 136.623Å
α: 90° β: 90.39° γ: 90°
R-values:
R R work R free
0.261 0.258 0.324
Expression systems:
  • Trichoplusia ni
  • Homo sapiens

Quick links

Citations

1 review citation

Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-CoV-2 Variants.
Cui et al. (2024)
11 other articles