› › Structure analysis

US28 bound to engineered chemokine CX3CL1.35 and nanobodies

X-ray diffraction
3.5Å resolution
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:
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: 28784.59 Å2
Buried surface area: 6649.47 Å2
Dissociation area: 905.05 Å2
Dissociation energy (ΔGdiss): 2.67 kcal/mol
Dissociation entropy (TΔSdiss): 12.06 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-230970

Macromolecules

G-protein coupled receptor homolog US28
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
Pfam: 7 transmembrane receptor (rhodopsin family)
InterPro:
G-protein coupled receptor homolog US28 in PDB entry 5wb2, assembly 1, front view.
G-protein coupled receptor homolog US28 in PDB entry 5wb2, assembly 1, side view.
G-protein coupled receptor homolog US28 in PDB entry 5wb2, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P69333  
146050100150200250300350400450
 
200400YKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNFLVIFTITWRRRIQ*SGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFYVAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQCMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIAVVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYVFVGTKFRQELH*LLAEFRLVPRGSGGSGGSLVPRGSQVQLVESGGGLVRPGGSLRLSCAASGSIFTIYAMGWYRQAPGKQRELVARITFGGDTNYADSVKGRFTISRDNAKNAVYLQMNSLKPEDTAVYYCNAEETIVEEADYWGQGTQVTVSSRALEVLF
UniProt
P69333
Chains
Domains
Secondary structure
Flexibility predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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Processed fractalkine
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
Pfam: Small cytokines (intecrine/chemokine), interleukin-8 like
InterPro:
CATH: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Processed fractalkine in PDB entry 5wb2, assembly 1, front view.
Processed fractalkine in PDB entry 5wb2, assembly 1, side view.
Processed fractalkine in PDB entry 5wb2, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P78423  
17610203040506070
 
204060LLPHANYCAITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQAAALTRNG
UniProt
P78423
Chains
Domains
Secondary structure
Flexibility predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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nanobody B1
Chain: D
Length: 131 amino acids
Theoretical weight: 14.15 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
InterPro:
nanobody B1 in PDB entry 5wb2, assembly 1, front view.
nanobody B1 in PDB entry 5wb2, assembly 1, side view.
nanobody B1 in PDB entry 5wb2, assembly 1, top view.
1131102030405060708090100110120130
 
50100*LQLVESGGGLVQPGGSLRLSCAASGYSLEYYAIGWFRQAPGKEREGVSCISTSVGSTKYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCGADLSTFYGGNYYCGDRGIYDYYGQGTQVTVSSRG
Chains
RSRZ Outlier Chain C (auth D)
Chain C (auth D)
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
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