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Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an intracellular Fab, and an extracellular Fab

Electron Microscopy
3.3Å resolution
PDB entry 7sk4 coloured by chain, front view.
PDB entry 7sk4 coloured by chain, side view.
PDB entry 7sk4 coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero hexamer (preferred)
Entry contents: 6 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero hexamer
Accessible surface area: 34651.27 Å2
Buried surface area: 15653.07 Å2
Dissociation area: 1,728.97 Å2
Dissociation energy (ΔGdiss): 5.79 kcal/mol
Dissociation entropy (TΔSdiss): 13.54 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-225547

Macromolecules

Atypical chemokine receptor 3
Chain: A
Length: 393 amino acids
Theoretical weight: 45.2 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P25106 (Residues: 2-362; Coverage: 100%)
Gene names: ACKR3, CMKOR1, CXCR7, GPR159, RDC1
Pfam: 7 transmembrane receptor (rhodopsin family)
InterPro:
Atypical chemokine receptor 3 in PDB entry 7sk4, assembly 1, front view.
Atypical chemokine receptor 3 in PDB entry 7sk4, assembly 1, side view.
Atypical chemokine receptor 3 in PDB entry 7sk4, assembly 1, top view.
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Stromal cell-derived factor 1
Chain: B
Length: 69 amino acids
Theoretical weight: 8.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P48061 (Residues: 22-89; Coverage: 94%)
Gene names: CXCL12, SDF1, SDF1A, SDF1B
Pfam: Small cytokines (intecrine/chemokine), interleukin-8 like
InterPro:
Stromal cell-derived factor 1 in PDB entry 7sk4, assembly 1, front view.
Stromal cell-derived factor 1 in PDB entry 7sk4, assembly 1, side view.
Stromal cell-derived factor 1 in PDB entry 7sk4, assembly 1, top view.
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CID25 Fab light chain
Chain: C
Length: 215 amino acids
Theoretical weight: 23.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
InterPro:
CID25 Fab light chain in PDB entry 7sk4, assembly 1, front view.
CID25 Fab light chain in PDB entry 7sk4, assembly 1, side view.
CID25 Fab light chain in PDB entry 7sk4, assembly 1, top view.
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CID25 Fab heavy chain
Chain: D
Length: 236 amino acids
Theoretical weight: 25.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
InterPro:
CID25 Fab heavy chain in PDB entry 7sk4, assembly 1, front view.
CID25 Fab heavy chain in PDB entry 7sk4, assembly 1, side view.
CID25 Fab heavy chain in PDB entry 7sk4, assembly 1, top view.
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CID24 Fab light chain
Chain: E
Length: 215 amino acids
Theoretical weight: 23.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
InterPro:
CID24 Fab light chain in PDB entry 7sk4, assembly 1, front view.
CID24 Fab light chain in PDB entry 7sk4, assembly 1, side view.
CID24 Fab light chain in PDB entry 7sk4, assembly 1, top view.
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CID24 Fab heavy chain
Chain: F
Length: 238 amino acids
Theoretical weight: 25.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
InterPro:
CID24 Fab heavy chain in PDB entry 7sk4, assembly 1, front view.
CID24 Fab heavy chain in PDB entry 7sk4, assembly 1, side view.
CID24 Fab heavy chain in PDB entry 7sk4, assembly 1, top view.
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