› 4xt1

X-ray diffraction
2.89Å resolution

Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1

Released:
DOI: 10.2210/pdb4xt1/pdb
PDB entry 4xt1 coloured by chain, front view.
PDB entry 4xt1 coloured by chain, side view.
PDB entry 4xt1 coloured by chain, top view.
Source organisms:
Primary publication:
Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor.
Burg JS, Ingram JR, Venkatakrishnan AJ, Jude KM, Dukkipati A, Feinberg EN, Angelini A, Waghray D, Dror RO, Ploegh HL, Garcia KC
Science 347 1113-7 (2015)
PMID: 25745166

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-229987 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
G-protein coupled receptor homolog US28 Chain: A
Molecule details ›
Chain: A
Length: 362 amino acids
Theoretical weight: 42.04 KDa
Source organism: Cytomegalovirus
Expression system: Homo sapiens
UniProt:
  • Canonical: P69332 (Residues: 1-354; Coverage: 100%)
Gene name: US28
Sequence domains: 7 transmembrane receptor (rhodopsin family)
Structure domains: Rhodopsin 7-helix transmembrane proteins
Processed fractalkine Chain: B
Molecule details ›
Chain: B
Length: 91 amino acids
Theoretical weight: 9.97 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P78423 (Residues: 25-101; Coverage: 21%)
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 7 Chain: C
Molecule details ›
Chain: C
Length: 134 amino acids
Theoretical weight: 14.62 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli BL21
Structure domains: Immunoglobulins

Ligands and Environments

4 bound ligands:
Ligand CLR 2 x CLR
Ligand OLC 6 x OLC
Ligand UNL 7 x UNL
Ligand SIN 1 x SIN
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: I4
Unit cell:
a: 81.024Å b: 81.024Å c: 231.303Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.199 0.249
Expression systems:
  • Homo sapiens
  • Escherichia coli BL21

Quick links

Citations

53 review citations

A guide to chemokines and their receptors.
Hughes et al. (2018)
52 more

41 mentions without citation

Nanobodies to Study G Protein-Coupled Receptor Structure and Function.
Manglik et al. (2017)
40 more