+Open data
-Basic information
Entry | Database: PDB / ID: 8k2w | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of CXCR3 complexed with antagonist AMG487 | |||||||||
Components |
| |||||||||
Keywords | SIGNALING PROTEIN / G protein coupled receptor / chemokine receptor / CXCR3 / AMG487 / complex | |||||||||
Function / homology | Function and homology information dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / regulation of leukocyte migration / sensory perception of temperature stimulus / positive regulation of eating behavior / C-X-C chemokine binding / adenylate cyclase-inhibiting opioid receptor signaling pathway / chemokine binding / G protein-coupled opioid receptor activity ...dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / regulation of leukocyte migration / sensory perception of temperature stimulus / positive regulation of eating behavior / C-X-C chemokine binding / adenylate cyclase-inhibiting opioid receptor signaling pathway / chemokine binding / G protein-coupled opioid receptor activity / 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 / C-C chemokine receptor activity / sensory perception / positive regulation of potassium ion transmembrane transport / conditioned place preference / C-C chemokine binding / positive regulation of chemotaxis / negative regulation of execution phase of apoptosis / maternal behavior / receptor serine/threonine kinase binding / neuropeptide 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 / neuropeptide signaling pathway / estrous cycle / regulation of cell adhesion / negative regulation of angiogenesis / MECP2 regulates neuronal receptors and channels / axon terminus / sensory perception of pain / T-tubule / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / cell chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / locomotory behavior / cellular response to glucose stimulus / electron transport chain / calcium-mediated signaling / 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 / signaling receptor activity / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cellular response to lipopolysaccharide / chemical synaptic transmission / postsynaptic membrane / perikaryon / angiogenesis / response to ethanol / defense response to virus / periplasmic space / cell surface receptor signaling pathway / electron transfer activity / cell adhesion / neuron projection / inflammatory response / iron ion binding / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / positive regulation of cell population proliferation / dendrite / heme binding / apoptotic process / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Lama glama (llama) Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Jiao, H.Z. / Hu, H.L. | |||||||||
Funding support | China, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8k2w.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8k2w.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 8k2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k2w_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8k2w_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8k2w_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 8k2w_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/8k2w ftp://data.pdbj.org/pub/pdb/validation_reports/k2/8k2w | HTTPS FTP |
-Related structure data
Related structure data | 36841MC 8k2xC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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.) Lama glama (llama) / Production host: Spodoptera frugiperda (fall armyworm) |
---|---|
#2: Protein | Mass: 56327.051 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: cybC, CXCR3, OPRK1, OPRK / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P0ABE7, UniProt: P49682, UniProt: P41145 |
-Non-polymers , 4 types, 4 molecules
#3: Chemical | ChemComp-CLR / |
---|---|
#4: Chemical | ChemComp-PCW / |
#5: Chemical | ChemComp-LPC / [ |
#6: Chemical | ChemComp-FI6 / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CXCR3-KOR-AMG487-Nb6 / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
---|---|
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 |
---|---|
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: 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 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 834686 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|