› 7sk5

Electron Microscopy
4Å resolution

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

Released:
DOI: 10.2210/pdb7sk5/pdb
PDB entry 7sk5 coloured by chain, front view.
PDB entry 7sk5 coloured by chain, side view.
PDB entry 7sk5 coloured by chain, top view.
Source organisms:
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-25173

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-225548 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 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)
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'
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
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'
Anti-Fab nanobody Chain: K
Molecule details ›
Chain: K
Length: 123 amino acids
Theoretical weight: 13.39 KDa
Source organism: Lama glama
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Ligands and Environments

1 bound ligand:
Ligand CLR 7 x CLR
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4Å
Relevant EMDB volumes: EMD-25173
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

2 mentions without citation

Regulation of polymerase II transcription by 7SK snRNA: two distinct RNA elements direct P-TEFb and HEXIM1 binding.
Egloff et al. (2006)
1 more