› 8u4o

Electron Microscopy
3.29Å resolution

Structure of CXCL12-bound CXCR4/Gi complex

Released:
DOI: 10.2210/pdb8u4o/pdb
PDB entry 8u4o coloured by chain, front view.
PDB entry 8u4o coloured by chain, side view.
PDB entry 8u4o coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into CXCR4 modulation and oligomerization.
Saotome K, McGoldrick LL, Ho JH, Ramlall TF, Shah S, Moore MJ, Kim JH, Leidich R, Olson WC, Franklin MC
Nat Struct Mol Biol (2024)
PMID: 39313635
Related structures: EMD-41889

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-245783 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
C-X-C chemokine receptor type 4; Green fluorescent protein Chain: R
Molecule details ›
Chain: R
Length: 632 amino acids
Theoretical weight: 71.06 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P61073 (Residues: 2-352; Coverage: 100%)
  • Canonical: P42212 (Residues: 1-238; Coverage: 100%)
Gene names: CXCR4, GFP
Sequence domains:
Guanine nucleotide-binding protein G(i) subunit alpha-1 Chain: A
Molecule details ›
Chain: A
Length: 365 amino acids
Theoretical weight: 41.59 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P63096 (Residues: 2-354; Coverage: 100%)
  • Best match: P63096-2 (Residues: 1-302)
Gene name: GNAI1
Sequence domains: G-protein alpha subunit
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 Chain: B
Molecule details ›
Chain: B
Length: 350 amino acids
Theoretical weight: 38.53 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P62873 (Residues: 2-340; Coverage: 100%)
Gene name: GNB1
Sequence domains: WD domain, G-beta repeat
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 Chain: C
Molecule details ›
Chain: C
Length: 71 amino acids
Theoretical weight: 7.86 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P59768 (Residues: 1-71; Coverage: 100%)
Gene name: GNG2
Sequence domains: GGL domain
Stromal cell-derived factor 1 Chain: J
Molecule details ›
Chain: J
Length: 68 amino acids
Theoretical weight: 7.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P48061 (Residues: 22-89; Coverage: 94%)
Gene names: CXCL12, SDF1, SDF1A, SDF1B
Sequence domains: Small cytokines (intecrine/chemokine), interleukin-8 like

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.29Å
Relevant EMDB volumes: EMD-41889
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli

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