› 5wb2

X-ray diffraction
3.5Å resolution

US28 bound to engineered chemokine CX3CL1.35 and nanobodies

Released:
DOI: 10.2210/pdb5wb2/pdb
Model geometry
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PDB entry 5wb2 coloured by chain, front view.
PDB entry 5wb2 coloured by chain, side view.
PDB entry 5wb2 coloured by chain, top view.
Source organisms:
Primary publication:
Viral GPCR US28 can signal in response to chemokine agonists of nearly unlimited structural degeneracy.
Miles TF, Spiess K, Jude KM, Tsutsumi N, Burg JS, Ingram JR, Waghray D, Hjorto GM, Larsen O, Ploegh HL, Rosenkilde MM, Garcia KC
OpenAccess logo Elife 7 (2018)
PMID: 29882741

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-230970 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
G-protein coupled receptor homolog US28 Chain: A
Molecule details ›
Chain: A
Length: 460 amino acids
Theoretical weight: 52.16 KDa
Source organism: Human betaherpesvirus 5
Expression system: Homo sapiens
UniProt:
  • Canonical: P69333 (Residues: 1-310; Coverage: 88%)
Gene name: US28
Sequence domains: 7 transmembrane receptor (rhodopsin family)
Processed fractalkine Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.63 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P78423 (Residues: 34-100; Coverage: 18%)
Gene names: A-152E5.2, CX3CL1, FKN, NTT, SCYD1
Sequence domains: Small cytokines (intecrine/chemokine), interleukin-8 like
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
nanobody B1 Chain: D

Ligands and Environments

4 bound ligands:
Ligand CLR 2 x CLR
Ligand OLC 4 x OLC
Ligand ZN 1 x ZN
Ligand MES 1 x MES
2 modified residues:
Ligand YCM 2 x YCM
Ligand PCA 1 x PCA

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21212
Unit cell:
a: 47.17Å b: 128.94Å c: 127.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.256 0.252 0.296
Expression systems:
  • Homo sapiens
  • Trichoplusia ni
  • Escherichia coli

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Citations

6 review citations

Advances in therapeutic peptides targeting G protein-coupled receptors.
Davenport et al. (2020)
5 more

8 mentions without citation

G protein-coupled receptors: structure- and function-based drug discovery.
Yang et al. (2021)
7 more

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