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Open data
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Basic information
Entry | Database: PDB / ID: 8k2w | |||||||||
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Title | Structure of CXCR3 complexed with antagonist AMG487 | |||||||||
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![]() | SIGNALING PROTEIN / G protein coupled receptor / chemokine receptor / CXCR3 / AMG487 / complex | |||||||||
Function / homology | ![]() dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / regulation of leukocyte migration / sensory perception of temperature stimulus / positive regulation of eating behavior / adenylate cyclase-inhibiting opioid receptor signaling pathway / C-X-C chemokine binding / G protein-coupled opioid receptor activity / chemokine binding ...dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / regulation of leukocyte migration / sensory perception of temperature stimulus / positive regulation of eating behavior / adenylate cyclase-inhibiting opioid receptor signaling pathway / C-X-C chemokine binding / G protein-coupled opioid receptor activity / chemokine binding / negative regulation of luteinizing hormone secretion / C-X-C chemokine receptor activity / G protein-coupled opioid receptor signaling pathway / chemokine receptor activity / positive regulation of dopamine secretion / sensory perception / positive regulation of potassium ion transmembrane transport / conditioned place preference / positive regulation of chemotaxis / C-C chemokine receptor activity / maternal behavior / negative regulation of execution phase of apoptosis / C-C chemokine binding / neuropeptide binding / receptor serine/threonine kinase binding / Chemokine receptors bind chemokines / positive regulation of p38MAPK cascade / eating behavior / positive regulation of execution phase of apoptosis / negative regulation of endothelial cell proliferation / behavioral response to cocaine / estrous cycle / neuropeptide signaling pathway / regulation of cell adhesion / axon terminus / MECP2 regulates neuronal receptors and channels / sensory perception of pain / T-tubule / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / negative regulation of angiogenesis / cell chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / locomotory behavior / calcium-mediated signaling / cellular response to glucose stimulus / electron transport chain / response to nicotine / response to insulin / adenylate cyclase-activating G protein-coupled receptor signaling pathway / synaptic vesicle membrane / response to estrogen / positive regulation of angiogenesis / chemotaxis / phospholipase C-activating G protein-coupled receptor signaling pathway / presynaptic membrane / signaling receptor activity / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / postsynaptic membrane / cellular response to lipopolysaccharide / perikaryon / angiogenesis / response to ethanol / defense response to virus / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / cell adhesion / inflammatory response / neuron projection / iron ion binding / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / apoptotic process / dendrite / heme binding / positive regulation of cell population proliferation / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
![]() | Jiao, H.Z. / Hu, H.L. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.6 KB | Display | ![]() |
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PDB format | ![]() | 69.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 36841MC ![]() 8k2xC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Antibody / Protein , 2 types, 2 molecules NR
#1: Antibody | Mass: 18665.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 56327.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: cybC, CXCR3, OPRK1, OPRK / Production host: ![]() ![]() References: UniProt: P0ABE7, UniProt: P49682, UniProt: P41145 |
-Non-polymers , 4 types, 4 molecules ![](data/chem/img/CLR.gif)
![](data/chem/img/PCW.gif)
![](data/chem/img/LPC.gif)
![](data/chem/img/FI6.gif)
![](data/chem/img/PCW.gif)
![](data/chem/img/LPC.gif)
![](data/chem/img/FI6.gif)
#3: Chemical | ChemComp-CLR / |
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#4: Chemical | ChemComp-PCW / |
#5: Chemical | ChemComp-LPC / [ |
#6: Chemical | ChemComp-FI6 / |
-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: CXCR3-KOR-AMG487-Nb6 / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
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 % |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 51.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 834686 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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