9UPU image
Deposition Date 2025-04-29
Release Date 2026-04-29
Last Version Date 2026-04-29
Entry Detail
PDB ID:
9UPU
Title:
Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a
Biological Source:
Source Organism(s):
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding pr
Gene (Uniprot):GNAI1
Chain IDs:C (auth: A)
Chain Length:354
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding pr
Gene (Uniprot):GNB1
Chain IDs:A (auth: B)
Chain Length:384
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding pr
Gene (Uniprot):GNG2
Chain IDs:B (auth: C)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Stromal cell-derived factor 1
Gene (Uniprot):CXCL12
Chain IDs:E (auth: J)
Chain Length:8
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Soluble cytochrome b562,C-X-C
Gene (Uniprot):cybC, CXCR4
Chain IDs:F (auth: R)
Chain Length:648
Number of Molecules:1
Biological Source:Escherichia coli, Homo sapiens, Oplophorus gracilirostris
Protein Blast
Polymer Type:polypeptide(L)
Molecule:single-chain variable fragmen
Chain IDs:D (auth: S)
Chain Length:259
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS.
Biorxiv ? ? ? (2025)
PMID: 40672153 DOI: 10.1101/2025.07.08.663251

Abstact

G-protein coupled receptors (GPCRs) are transmembrane proteins that mediate a range of signaling functions and, therefore, offer targets for a number of therapeutic interventions. Chemokine receptor CXCR4, a GPCR, plays versatile roles in normal and abnormal physiological processes. Synthetic CXCR4 antagonists have been extensively studied and approved for the clinical treatment of cancer and other diseases. We recently elucidated the structural mechanisms underlying CXCR4 antagonism using cryogenic electron microscopy (cryo-EM). CXCR4 agonism by synthetic molecules is an unanticipated therapeutic intervention we recently unveiled. The structural mechanisms underlying those actions remain poorly understood yet could help elucidate a new class of drugs. Here we demonstrate a synthetic dual-moiety strategy that combines simplified agonistic and antagonistic moieties taken from natural agonistic and antagonistic chemokines, respectively, to design de novo peptide mimics of biological function of natural CXCR4 agonist SDF-1alpha. Two peptides so generated, SDV1a and SDVX1 were shown to mimic the action of SDF-1alpha in activating CXCR4 signaling pathways and cell migration. The structural mechanism of these peptides in the mimicry of CXCR4 agonism was illustrated by cryo-EM structures of CXCR4 bound and activated by the peptides in the presence of G protein, revealing common interactions with the receptor by these peptides in comparison with SDF-1alpha that explain their close mimicry and conformational changes leading to CXCR4 signal activation. The therapeutic benefit of one of these peptides, SDV1a, was demonstrated in the SOD1(G93A) mouse model of the spinal motor neuron degenerative disease, amyotrophic lateral sclerosis (ALS) wherein the success of neuroprotective actions of transplanted human neural stem cells (hNSCs) is directly correlated with the expanse of diseased neuroaxis traversed by the donor cells; SDV1a enabled broader neuroprotective coverage while also permitting a much less invasive route of cell administration for extending life. Taken together, these results provide insights into the structural determinants of therapeutic CXCR4 agonism which may allow the design of adjunctive drugs that improve cell-based treatments of central nervous system (CNS) diseases.

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Primary Citation of related structures
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