› 7ps5

X-ray diffraction
3.14Å resolution

Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-47 Fab

Released:
DOI: 10.2210/pdb7ps5/pdb
PDB entry 7ps5 coloured by chain, front view.
PDB entry 7ps5 coloured by chain, side view.
PDB entry 7ps5 coloured by chain, top view.
Source organisms:
Primary publication:
The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Liu C, Zhou D, Nutalai R, Duyvesteyn HME, Tuekprakhon A, Ginn HM, Dejnirattisai W, Supasa P, Mentzer AJ, Wang B, Case JB, Zhao Y, Skelly DT, Chen RE, Johnson SA, Ritter TG, Mason C, Malik T, Temperton N, Paterson NG, Williams MA, Hall DR, Clare DK, Howe A, Goulder PJR, Fry EE, Diamond MS, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR
OpenAccess logo Cell Host Microbe 30 53-68.e12 (2022)
PMID: 34921776

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-209888 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Beta-47 Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 228 amino acids
Theoretical weight: 24.44 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Beta-47 Fab light chain Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.59 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Spike protein S1 Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 23.65 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 333-526; Coverage: 15%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 78.101Å b: 114.409Å c: 168.972Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.226 0.274
Expression system: Homo sapiens

Quick links

Citations

9 review citations

SARS-CoV-2: Evolution and Emergence of New Viral Variants.
Flores-Vega et al. (2022)
8 more

2 mentions without citation

The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Liu et al. (2022)
1 more