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- EMDB-71079: Composite map of CXCL9-CXCR3-Gi-scFv16 -

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Basic information

Entry
Database: EMDB / ID: EMD-71079
TitleComposite map of CXCL9-CXCR3-Gi-scFv16
Map dataComposite map of CXCL9-CXCR3-Gi-scFv16
Sample
  • Complex: CXCR3, CXCL9, Gi
  • Protein or peptide: C-X-C chemokine receptor type 3,GFP-like fluorescent chromoprotein FP506, related
  • Protein or peptide: C-X-C motif chemokine 9
  • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
  • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
  • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Protein or peptide: scFV16
KeywordsGPCR / chemokine receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


CXCR3 chemokine receptor binding / regulation of leukocyte migration / chemokine binding / C-X-C chemokine binding / chemokine receptor activity / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / positive regulation of chemotaxis / T cell chemotaxis / C-C chemokine receptor activity ...CXCR3 chemokine receptor binding / regulation of leukocyte migration / chemokine binding / C-X-C chemokine binding / chemokine receptor activity / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / positive regulation of chemotaxis / T cell chemotaxis / C-C chemokine receptor activity / C-C chemokine binding / negative regulation of execution phase of apoptosis / chemokine activity / Chemokine receptors bind chemokines / positive regulation of myoblast fusion / negative regulation of endothelial cell proliferation / positive regulation of execution phase of apoptosis / positive regulation of myoblast differentiation / regulation of cell adhesion / cellular defense response / 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 / cytokine activity / cellular response to forskolin / bioluminescence / positive regulation of release of sequestered calcium ion into cytosol / regulation of mitotic spindle organization / chemokine-mediated signaling pathway / cell chemotaxis / generation of precursor metabolites and energy / Regulation of insulin secretion / calcium-mediated signaling / neuropeptide signaling pathway / defense response / response to prostaglandin E / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / G alpha (12/13) signalling events / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / sensory perception of taste / Thrombin signalling through proteinase activated receptors (PARs) / sperm principal piece / adenylate cyclase-activating G protein-coupled receptor signaling pathway / signaling receptor complex adaptor activity / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / signaling receptor activity / retina development in camera-type eye
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 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 / C-X-C motif chemokine 9 / GFP-like fluorescent chromoprotein FP506, related
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSun D / Masureel M / Johnson M
Funding support1 items
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, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71079.png

Downloads & links

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Map

FileDownload / File: emd_71079.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of CXCL9-CXCR3-Gi-scFv16
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.46 Å/pix.
x 320 pix.
= 467.84 Å		1.46 Å/pix.
x 320 pix.
= 467.84 Å		1.46 Å/pix.
x 320 pix.
= 467.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.462 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.276
Minimum - Maximum-1.4912543 - 2.43564
Average (Standard dev.)0.000049772723 (±0.029999958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 467.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CXCR3, CXCL9, Gi

EntireName: CXCR3, CXCL9, Gi
Components
  • Complex: CXCR3, CXCL9, Gi
  • Protein or peptide: C-X-C chemokine receptor type 3,GFP-like fluorescent chromoprotein FP506, related
  • Protein or peptide: C-X-C motif chemokine 9
  • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
  • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
  • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Protein or peptide: scFV16

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Supramolecule #1: CXCR3, CXCL9, Gi

SupramoleculeName: CXCR3, CXCL9, Gi / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: C-X-C chemokine receptor type 3,GFP-like fluorescent chromoprotei...

MacromoleculeName: C-X-C chemokine receptor type 3,GFP-like fluorescent chromoprotein FP506, related
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.79268 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKGSENLY FQSGSMVLEV SDHQVLNDAE VAALLENFSS SYDYGENESD SCCTSPPCPQ DFSLNFDRA FLPALYSLLF LLGLLGNGAV AAVLLSRRTA LSSTDTFLLH LAVADTLLVL TLPLWAVDAA VQWVFGSGLC K VAGALFNI ...String:
MKTIIALSYI FCLVFADYKD DDDKGSENLY FQSGSMVLEV SDHQVLNDAE VAALLENFSS SYDYGENESD SCCTSPPCPQ DFSLNFDRA FLPALYSLLF LLGLLGNGAV AAVLLSRRTA LSSTDTFLLH LAVADTLLVL TLPLWAVDAA VQWVFGSGLC K VAGALFNI NFYAGALLLA CISFDRYLNI VHATQLYRRG PPARVTLTCL AVWGLCLLFA LPDFIFLSAH HDERLNATHC QY NFPQVGR TALRVLQLVA GFLLPLLVMA YCYAHILAVL LVSRGQRRLR AMRLVVVAVV AFALCWTPYH LVVLVDILMD LGA LARNCG RESRVDVAKS VTSGLGYMHC CLNPLLYAFV GVKFRERMWM LLLRLGCPNQ RGLQRQPSSS RRDSSWSETS EASY SGLGN SLEVLFQGPM VSKGEELFTG VVPILVELDG DVNGHKFSVS GEGEGDATYG KLTLKLICTT GKLPVPWPTL VTTLG YGLQ CFARYPDHMK QHDFFKSAMP EGYVQERTIF FKDDGNYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNY NSH NVYITADKQK NGIKANFKIR HNIEDGGVQL ADHYQQNTPI GDGPVLLPDN HYLSYQSKLS KDPNEKRDHM VLLEFVT AA GITLGMDELY KGSAWSHPQF EKGGGSGGGS GGSAWSHPQF EK

UniProtKB: C-X-C chemokine receptor type 3, GFP-like fluorescent chromoprotein FP506, related

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Macromolecule #2: C-X-C motif chemokine 9

MacromoleculeName: C-X-C motif chemokine 9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.7539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TPVVRKGRCS CISTNQGTIH LQSLKDLKQF APSPSCEKIE IIATLKNGVQ TCLNPDSADV KELIKKWEKQ VSQKKKQKNG KKHQKKKVL KVRKSQRSRQ KKTT

UniProtKB: C-X-C motif chemokine 9

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

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.182078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKHHHHHHH HHHENLYFQG GSMGCTLSAE DKAAVERSKM IDRNLREDGE KAAREVKLLL LGAGESGKST IVKQMKIIHE AGYSEEECK QYKAVVYSNT IQSIIAIIRA MGRLKIDFGD SARADDARQL FVLAGAAEEG FMTAELAGVI KRLWKDSGVQ A CFNRSREY ...String:
MKKHHHHHHH HHHENLYFQG GSMGCTLSAE DKAAVERSKM IDRNLREDGE KAAREVKLLL LGAGESGKST IVKQMKIIHE AGYSEEECK QYKAVVYSNT IQSIIAIIRA MGRLKIDFGD SARADDARQL FVLAGAAEEG FMTAELAGVI KRLWKDSGVQ A CFNRSREY QLNDSAAYYL NDLDRIAQPN YIPTQQDVLR TRVKTTGIVE THFTFKDLHF KMFDVGGQRS ERKKWIHCFE GV TAIIFCV ALSDYDLVLA EDEEMNRMHE SMKLFDSICN NKWFTDTSII LFLNKKDLFE EKIKKSPLTI CYPEYAGSNT YEE AAAYIQ CQFEDLNKRK DTKEIYTHFT CATDTKNVQF VFDAVTDVII KNNLKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.518121 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHG ENLYFQGSSE LDQLRQEAEQ LKNQIRDARK ACADATLSQI TNNIDPVGRI QMRTRRTLRG HLAKIYAMHW GTDSRLLVS ASQDGKLIIW DSYTTNKVHA IPLRSSWVMT CAYAPSGNYV ACGGLDNICS IYNLKTREGN VRVSRELAGH T GYLSCCRF ...String:
MHHHHHHHHG ENLYFQGSSE LDQLRQEAEQ LKNQIRDARK ACADATLSQI TNNIDPVGRI QMRTRRTLRG HLAKIYAMHW GTDSRLLVS ASQDGKLIIW DSYTTNKVHA IPLRSSWVMT CAYAPSGNYV ACGGLDNICS IYNLKTREGN VRVSRELAGH T GYLSCCRF LDDNQIVTSS GDTTCALWDI ETGQQTTTFT GHTGDVMSLS LAPDTRLFVS GACDASAKLW DVREGMCRQT FT GHESDIN AICFFPNGNA FATGSDDATC RLFDLRADQE LMTYSHDNII CGITSVSFSK SGRLLLAGYD DFNCNVWDAL KAD RAGVLA GHDNRVSCLG VTDDGMAVAT GSWDSFLKIW N

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #6: scFV16

MacromoleculeName: scFV16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 28.754949 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AGSDVQLVES GGGLVQPGGS RKLSCSASGF AFSSFGMHWV RQAPEKGLEW VAYISSGSGT IYYADTVKGR FTISRDDPKN TLFLQMTSL RSEDTAMYYC VRSIYYYGSS PFDFWGQGTT LTVSSGGGSG GGSGGGGSDI VMTQATSSVP VTPGESVSIS C RSSKSLLH ...String:
AGSDVQLVES GGGLVQPGGS RKLSCSASGF AFSSFGMHWV RQAPEKGLEW VAYISSGSGT IYYADTVKGR FTISRDDPKN TLFLQMTSL RSEDTAMYYC VRSIYYYGSS PFDFWGQGTT LTVSSGGGSG GGSGGGGSDI VMTQATSSVP VTPGESVSIS C RSSKSLLH SNGNTYLYWF LQRPGQSPQL LIYRMSNLAS GVPDRFSGSG SGTAFTLTIS RLEAEDVGVY YCMQHLEYPL TF GAGTKLE LKAAAGNSLV PRGSHHHHHH HH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 51645
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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