› 8wku

X-ray diffraction
3.5Å resolution

Complex structure of MjHKU4r-CoV-1 spike RBD bound to human CD26

Released:
DOI: 10.2210/pdb8wku/pdb
PDB entry 8wku coloured by chain, front view.
PDB entry 8wku coloured by chain, side view.
PDB entry 8wku coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for receptor recognition and broad host tropism for merbecovirus MjHKU4r-CoV-1.
Zhao Z, Li X, Chai Y, Liu Z, Wang Q, Gao GF
OpenAccess logo EMBO Rep (2024)
PMID: 38877169

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, from a polypeptide, preferentially when Yaa is Pro, provided Zaa is neither Pro nor hydroxyproline.
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-499000 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (8 distinct):
Dipeptidyl peptidase 4 Chain: A
Molecule details ›
Chain: A
Length: 734 amino acids
Theoretical weight: 85.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P27487 (Residues: 39-766; Coverage: 95%)
Gene names: ADCP2, CD26, DPP4
Sequence domains:
Spike glycoprotein Chain: B
Molecule details ›
Chain: B
Length: 246 amino acids
Theoretical weight: 27.25 KDa
Source organism: Manis javanica
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: A0AAE8ZFM2 (Residues: 375-614; Coverage: 18%)
Gene name: S

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, FUC, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, FUC, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL02U1
Spacegroup: P3221
Unit cell:
a: 127.501Å b: 127.501Å c: 245.633Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.229 0.211 0.238
Expression systems:
  • Homo sapiens
  • Spodoptera frugiperda

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