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- PDB-9p0l: Composite map of CXCL10-CXCR3-Gi-scFv16 -

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Basic information

Entry
Database: PDB / ID: 9p0l
TitleComposite map of CXCL10-CXCR3-Gi-scFv16
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • C-X-C chemokine receptor type 3,GFP-like fluorescent chromoprotein FP506, related
  • C-X-C motif chemokine 10
  • scFv16
KeywordsMEMBRANE PROTEIN / GPCR / chemokine receptor
Function / homology
Function and homology information


regulation of T cell chemotaxis / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of leukocyte migration / chemokine binding / C-X-C chemokine binding / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / chemokine receptor activity / CXCR chemokine receptor binding ...regulation of T cell chemotaxis / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of leukocyte migration / chemokine binding / C-X-C chemokine binding / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / chemokine receptor activity / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / cAMP-dependent protein kinase regulator activity / response to auditory stimulus / negative regulation of myoblast differentiation / positive regulation of chemotaxis / T cell chemotaxis / C-C chemokine receptor activity / C-C chemokine binding / negative regulation of execution phase of apoptosis / positive regulation of monocyte chemotaxis / endothelial cell activation / response to vitamin D / chemokine activity / Chemokine receptors bind chemokines / muscle organ development / blood circulation / negative regulation of endothelial cell proliferation / chemoattractant activity / Interleukin-10 signaling / positive regulation of execution phase of apoptosis / positive regulation of T cell migration / regulation of cell adhesion / neutrophil chemotaxis / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / T cell migration / positive regulation of relaxation of smooth muscle / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / negative regulation of angiogenesis / antiviral innate immune response / cellular response to forskolin / bioluminescence / positive regulation of release of sequestered calcium ion into cytosol / regulation of mitotic spindle organization / chemokine-mediated signaling pathway / response to gamma radiation / cell chemotaxis / generation of precursor metabolites and energy / Regulation of insulin secretion / calcium-mediated signaling / neuropeptide signaling pathway / response to prostaglandin E / cellular response to virus / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / chemotaxis / centriolar satellite / G-protein beta/gamma-subunit complex binding / positive regulation of angiogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G beta:gamma signalling through BTK / photoreceptor disc membrane / ADP signalling through P2Y purinoceptor 12 / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / GDP binding / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / cell-cell signaling / regulation of cell population proliferation / adenylate cyclase-activating dopamine receptor signaling pathway / heparin binding / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus
Similarity search - Function
CXC chemokine receptor 3 / CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine receptor family / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily ...CXC chemokine receptor 3 / CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine receptor family / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / : / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / G-protein alpha subunit, group I / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
C-X-C motif chemokine 10 / C-X-C chemokine receptor type 3 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / GFP-like fluorescent chromoprotein FP506, related
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSun, D. / Masureel, M. / Johnson, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2026
Title: Molecular basis of CXC chemokine receptor 3 ligand multispecificity.
Authors: Alexandre Bouyssou / Dawei Sun / Tricia Zhou / Shannon Smith / Hoangdung Ho / Matthew Johnson / Caleigh Azumaya / Sigrid Noreng / Peter Liu / Shu Ti / Prajakta Joshi / Christine Tam / Ying ...Authors: Alexandre Bouyssou / Dawei Sun / Tricia Zhou / Shannon Smith / Hoangdung Ho / Matthew Johnson / Caleigh Azumaya / Sigrid Noreng / Peter Liu / Shu Ti / Prajakta Joshi / Christine Tam / Ying Yang / Eric Janezic / Laëtitia Comps-Agrar / Matthieu Masureel /
Abstract: C-X-C motif chemokine receptor 3 (CXCR3) is essential for immune cell functions and pivotal in T helper 1 cell infiltration in autoimmune and chronic inflammatory diseases and in tumor proliferation ...C-X-C motif chemokine receptor 3 (CXCR3) is essential for immune cell functions and pivotal in T helper 1 cell infiltration in autoimmune and chronic inflammatory diseases and in tumor proliferation and metastasis, but the mechanisms by which the endogenous ligands CXCL9, CXCL10, and CXCL11 differentially recognize and activate CXCR3 are not fully understood. Here, we present cryo-electron microscopy structures of all three chemokine-CXCR3-G complexes, complemented by cell binding studies and functional mutagenesis data. We systematically compare the pharmacological and interaction profiles of CXCL9, CXCL10, and CXCL11 to rationalize their varying efficacies and potencies and to reveal the critical role of the membrane-distal CXCR3 N terminus in ligand binding and signaling. Using chimeric chemokines and molecular dynamics, we reveal the signaling plasticity of chemokine ligands and signaling determinants. Together, these insights enable us to propose a multimodal binding and activation framework that explains CXCR3 chemokine ligand multispecificity and signaling versatility and offer tools to interrogate and modulate CXCR3 biology.
History
DepositionJun 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-X-C chemokine receptor type 3,GFP-like fluorescent chromoprotein FP506, related
B: C-X-C motif chemokine 10
C: Guanine nucleotide-binding protein G(i) subunit alpha-1
D: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
E: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
F: scFv16


Theoretical massNumber of molelcules
Total (without water)203,7726
Polymers203,7726
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein C-X-C chemokine receptor type 3,GFP-like fluorescent chromoprotein FP506, related / CXC-R3 / CXCR-3 / CKR-L2 / G protein-coupled receptor 9 / Interferon-inducible protein 10 receptor ...CXC-R3 / CXCR-3 / CKR-L2 / G protein-coupled receptor 9 / Interferon-inducible protein 10 receptor / IP-10 receptor


Mass: 75792.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCR3, GPR9, EAH_00062270 / Production host: Homo sapiens (human) / References: UniProt: P49682, UniProt: U6GSR1
#2: Protein C-X-C motif chemokine 10 / 10 kDa interferon gamma-induced protein / Gamma-IP10 / IP-10 / Small-inducible cytokine B10


Mass: 8663.343 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL10, INP10, SCYB10 / Production host: Escherichia coli (E. coli) / References: UniProt: P02778

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules CDE

#3: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1


Mass: 43182.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63096
#4: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1


Mass: 39518.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#5: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768

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Antibody , 1 types, 1 molecules F

#6: Antibody scFv16


Mass: 28754.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CXCR3, CXCL10, Gi / Type: COMPLEX / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 101131 / Symmetry type: POINT

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