+Open data
-Basic information
Entry | Database: PDB / ID: 8k2x | |||||||||
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Title | CXCR3-DNGi complex activated by CXCL10 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / G protein coupled receptor / chemokine receptor / CXCR3 / CXCL10 / complex | |||||||||
Function / homology | Function and homology information regulation of T cell chemotaxis / negative regulation of myoblast fusion / Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / CXCR3 chemokine receptor binding / regulation of leukocyte migration / C-X-C chemokine binding / chemokine binding / C-X-C chemokine receptor activity / chemokine receptor activity ...regulation of T cell chemotaxis / negative regulation of myoblast fusion / Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / CXCR3 chemokine receptor binding / regulation of leukocyte migration / C-X-C chemokine binding / chemokine binding / C-X-C chemokine receptor activity / chemokine receptor activity / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / CXCR chemokine receptor binding / response to auditory stimulus / C-C chemokine receptor activity / cAMP-dependent protein kinase regulator activity / C-C chemokine binding / positive regulation of chemotaxis / negative regulation of execution phase of apoptosis / negative regulation of myoblast differentiation / T cell chemotaxis / response to vitamin D / positive regulation of monocyte chemotaxis / chemokine-mediated signaling pathway / blood circulation / Chemokine receptors bind chemokines / endothelial cell activation / chemokine activity / muscle organ development / chemoattractant activity / positive regulation of execution phase of apoptosis / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / positive regulation of T cell migration / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / regulation of cell adhesion / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / antiviral innate immune response / regulation of mitotic spindle organization / cellular response to forskolin / neutrophil chemotaxis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / bioluminescence / negative regulation of angiogenesis / cell chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / Regulation of insulin secretion / G protein-coupled receptor binding / response to gamma radiation / electron transport chain / calcium-mediated signaling / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / cellular response to virus / response to peptide hormone / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / positive regulation of angiogenesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / GDP binding / chemotaxis / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / antimicrobial humoral immune response mediated by antimicrobial peptide / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) Oplophorus gracilirostris (crustacean) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Jiao, H.Z. / Hu, H.L. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Discov / Year: 2023 Title: Structure basis for the modulation of CXC chemokine receptor 3 by antagonist AMG487. Authors: Haizhan Jiao / Bin Pang / Ying-Chih Chiang / Qiang Chen / Qi Pan / Ruobing Ren / Hongli Hu / | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k2x.cif.gz | 248.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k2x.ent.gz | 187.2 KB | Display | PDB format |
PDBx/mmJSON format | 8k2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/8k2x ftp://data.pdbj.org/pub/pdb/validation_reports/k2/8k2x | HTTPS FTP |
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-Related structure data
Related structure data | 36842MC 8k2wC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG
#1: Protein | Mass: 40445.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63096 |
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#2: Protein | Mass: 42005.895 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 |
#3: Protein | 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 |
-Protein , 2 types, 2 molecules RL
#4: Protein | Mass: 72918.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human), (gene. exp.) Oplophorus gracilirostris (crustacean) Gene: cybC, CXCR3, GPR9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P0ABE7, UniProt: P49682, UniProt: Q9GV45, Oplophorus-luciferin 2-monooxygenase |
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#6: Protein | Mass: 10898.089 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02778 |
-Antibody / Non-polymers , 2 types, 2 molecules S
#5: Antibody | Mass: 27784.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oplophorus gracilirostris (crustacean) / Production host: Spodoptera frugiperda (fall armyworm) |
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#7: Chemical | ChemComp-CLR / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CXCR3-CXCL10-DNGi-scFv16 / Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 53.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110236 / Symmetry type: POINT |