› 7sk3

Electron Microscopy
3.8Å resolution

Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an extracellular Fab

Released:
DOI: 10.2210/pdb7sk3/pdb
PDB entry 7sk3 coloured by chain, front view.
PDB entry 7sk3 coloured by chain, side view.
PDB entry 7sk3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias.
Yen YC, Schafer CT, Gustavsson M, Eberle SA, Dominik PK, Deneka D, Zhang P, Schall TJ, Kossiakoff AA, Tesmer JJG, Handel TM
Sci Adv 8 eabn8063 (2022)
PMID: 35857509
Related structures: EMD-25171

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-225546 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Atypical chemokine receptor 3 Chain: A
Molecule details ›
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
Sequence domains: 7 transmembrane receptor (rhodopsin family)
Stromal cell-derived factor 1 Chain: B
Molecule details ›
Chain: B
Length: 68 amino acids
Theoretical weight: 7.98 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
Sequence domains: Small cytokines (intecrine/chemokine), interleukin-8 like
CID25 Fab light chain Chain: C
Molecule details ›
Chain: C
Length: 215 amino acids
Theoretical weight: 23.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
CID25 Fab heavy chain Chain: D
Molecule details ›
Chain: D
Length: 236 amino acids
Theoretical weight: 25.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
CID24 Fab light chain Chain: E
Molecule details ›
Chain: E
Length: 215 amino acids
Theoretical weight: 23.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
CID24 Fab heavy chain Chain: F
Molecule details ›
Chain: F
Length: 238 amino acids
Theoretical weight: 25.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Ligands and Environments

1 bound ligand:
Ligand CLR 8 x CLR
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-25171
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

6 review citations

The chemokines CXCL8 and CXCL12: molecular and functional properties, role in disease and efforts towards pharmacological intervention.
Cambier et al. (2023)
5 more

3 mentions without citation

Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias.
Yen et al. (2022)
2 more