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

X-ray diffraction
2.886Å resolution
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:
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero trimer
Accessible surface area: 23340.3 Å2
Buried surface area: 8490.36 Å2
Dissociation area: 1,133.54 Å2
Dissociation energy (ΔGdiss): 13.14 kcal/mol
Dissociation entropy (TΔSdiss): 11.93 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-229987

Macromolecules

G-protein coupled receptor homolog US28
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
Pfam: 7 transmembrane receptor (rhodopsin family)
InterPro:
CATH: Rhodopsin 7-helix transmembrane proteins
G-protein coupled receptor homolog US28 in PDB entry 4xt1, assembly 1, front view.
G-protein coupled receptor homolog US28 in PDB entry 4xt1, assembly 1, side view.
G-protein coupled receptor homolog US28 in PDB entry 4xt1, assembly 1, top view.
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Processed fractalkine
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
Pfam: Small cytokines (intecrine/chemokine), interleukin-8 like
InterPro:
CATH: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Processed fractalkine in PDB entry 4xt1, assembly 1, front view.
Processed fractalkine in PDB entry 4xt1, assembly 1, side view.
Processed fractalkine in PDB entry 4xt1, assembly 1, top view.
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nanobody 7
Chain: C
Length: 134 amino acids
Theoretical weight: 14.62 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli BL21
InterPro:
CATH: Immunoglobulins
nanobody 7 in PDB entry 4xt1, assembly 1, front view.
nanobody 7 in PDB entry 4xt1, assembly 1, side view.
nanobody 7 in PDB entry 4xt1, assembly 1, top view.
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