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- PDB-8k2w: Structure of CXCR3 complexed with antagonist AMG487 -

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Basic information

Entry
Database: PDB / ID: 8k2w
TitleStructure of CXCR3 complexed with antagonist AMG487
Components
  • Nb6
  • Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-type opioid receptor
KeywordsSIGNALING PROTEIN / G protein coupled receptor / chemokine receptor / CXCR3 / AMG487 / complex
Function / homology
Function and homology information


response to acrylamide / adenylate cyclase-inhibiting opioid receptor signaling pathway / dynorphin receptor activity / regulation of saliva secretion / regulation of leukocyte migration / negative regulation of luteinizing hormone secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / chemokine binding / C-X-C chemokine binding ...response to acrylamide / adenylate cyclase-inhibiting opioid receptor signaling pathway / dynorphin receptor activity / regulation of saliva secretion / regulation of leukocyte migration / negative regulation of luteinizing hormone secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / chemokine binding / C-X-C chemokine binding / G protein-coupled opioid receptor activity / chemokine receptor activity / G protein-coupled opioid receptor signaling pathway / C-X-C chemokine receptor activity / positive regulation of dopamine secretion / sensory perception / C-C chemokine receptor activity / positive regulation of potassium ion transmembrane transport / positive regulation of chemotaxis / receptor serine/threonine kinase binding / C-C chemokine binding / maternal behavior / conditioned place preference / negative regulation of execution phase of apoptosis / neuropeptide binding / positive regulation of p38MAPK cascade / Chemokine receptors bind chemokines / eating behavior / negative regulation of endothelial cell proliferation / behavioral response to cocaine / positive regulation of execution phase of apoptosis / neuropeptide signaling pathway / regulation of cell adhesion / estrous cycle / MECP2 regulates neuronal receptors and channels / axon terminus / sensory perception of pain / T-tubule / negative regulation of angiogenesis / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / cell chemotaxis / locomotory behavior / response to insulin / response to nicotine / calcium-mediated signaling / electron transport chain / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / response to estrogen / adenylate cyclase-activating G protein-coupled receptor signaling pathway / synaptic vesicle membrane / positive regulation of angiogenesis / chemotaxis / signaling receptor activity / presynaptic membrane / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / angiogenesis / chemical synaptic transmission / defense response to virus / perikaryon / response to ethanol / postsynaptic membrane / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / neuron projection / cell adhesion / immune response / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / external side of plasma membrane / apoptotic process / positive regulation of cell population proliferation / heme binding / dendrite / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CXC chemokine receptor 3 / Kappa opioid receptor / Opioid receptor / Chemokine receptor family / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...CXC chemokine receptor 3 / Kappa opioid receptor / Opioid receptor / Chemokine receptor family / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
CHOLESTEROL / Chem-FI6 / [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Soluble cytochrome b562 / Kappa-type opioid receptor / C-X-C chemokine receptor type 3
Similarity search - Component
Biological speciesLama glama (llama)
Escherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsJiao, H.Z. / Hu, H.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100963 China
Other privateGanghong Young Scholar Development Fund
CitationJournal: 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
DepositionJul 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: Nb6
R: Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-type opioid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2396
Polymers74,9932
Non-polymers2,2464
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Antibody / Protein , 2 types, 2 molecules NR

#1: Antibody Nb6


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 Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-type opioid receptor / Cytochrome b-562 / K-OR-1 / KOR-1


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

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Non-polymers , 4 types, 4 molecules

#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Chemical ChemComp-LPC / [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE


Mass: 468.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H47NO7P
#6: Chemical ChemComp-FI6 / N-[(1R)-1-[3-(4-ethoxyphenyl)-4-oxidanylidene-pyrido[2,3-d]pyrimidin-2-yl]ethyl]-N-(pyridin-3-ylmethyl)-2-[4-(trifluoromethyloxy)phenyl]ethanamide / (+/-)-AMG 487


Mass: 603.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H28F3N5O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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-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 solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 recordingElectron dose: 51.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 834686 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033212
ELECTRON MICROSCOPYf_angle_d0.5784365
ELECTRON MICROSCOPYf_dihedral_angle_d7.372553
ELECTRON MICROSCOPYf_chiral_restr0.039507
ELECTRON MICROSCOPYf_plane_restr0.004522

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