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- EMDB-36841: Structure of CXCR3 complexed with antagonist AMG487 -

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Basic information

Entry
Database: EMDB / ID: EMD-36841
TitleStructure of CXCR3 complexed with antagonist AMG487
Map data
Sample
  • Complex: CXCR3-KOR-AMG487-Nb6
    • Protein or peptide: Nb6
    • Protein or peptide: Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-type opioid receptor
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE
  • Ligand: 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
KeywordsG protein coupled receptor / chemokine receptor / CXCR3 / AMG487 / complex / SIGNALING PROTEIN
Function / homology
Function and homology information


response to acrylamide / regulation of saliva secretion / regulation of leukocyte migration / dynorphin receptor activity / 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 ...response to acrylamide / regulation of saliva secretion / regulation of leukocyte migration / dynorphin receptor activity / 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 / chemokine receptor activity / G protein-coupled opioid receptor signaling pathway / positive regulation of dopamine secretion / C-C chemokine receptor activity / sensory perception / positive regulation of potassium ion transmembrane transport / C-C chemokine binding / positive regulation of chemotaxis / negative regulation of execution phase of apoptosis / maternal behavior / conditioned place preference / receptor serine/threonine kinase binding / neuropeptide binding / Chemokine receptors bind chemokines / positive regulation of p38MAPK cascade / eating behavior / negative regulation of endothelial cell proliferation / positive regulation of execution phase of apoptosis / behavioral response to cocaine / neuropeptide signaling pathway / estrous cycle / regulation of cell adhesion / MECP2 regulates neuronal receptors and channels / axon terminus / sensory perception of pain / T-tubule / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / negative regulation of angiogenesis / 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 / response to nicotine / calcium-mediated signaling / electron transport chain / 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 / perikaryon / angiogenesis / defense response to virus / postsynaptic membrane / response to ethanol / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / cell adhesion / neuron projection / inflammatory response / immune response / iron ion binding / G protein-coupled receptor signaling pathway / external side of plasma membrane / dendrite / heme binding / positive regulation of cell population proliferation / apoptotic process / 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
Soluble cytochrome b562 / Kappa-type opioid receptor / C-X-C chemokine receptor type 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsJiao HZ / Hu HL
Funding support China, 2 items
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, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36841.png

Downloads & links

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Map

FileDownload / File: emd_36841.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.82
Minimum - Maximum-5.902996 - 8.506303000000001
Average (Standard dev.)-0.001972959 (±0.15240528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpen map

Fileemd_36841_additional_1.map
Annotationunsharpen map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36841_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36841_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : CXCR3-KOR-AMG487-Nb6

EntireName: CXCR3-KOR-AMG487-Nb6
Components
  • Complex: CXCR3-KOR-AMG487-Nb6
    • Protein or peptide: Nb6
    • Protein or peptide: Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-type opioid receptor
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE
  • Ligand: 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

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Supramolecule #1: CXCR3-KOR-AMG487-Nb6

SupramoleculeName: CXCR3-KOR-AMG487-Nb6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nb6

MacromoleculeName: Nb6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 18.665906 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAMA QVQLQESGGG LVQAGESLRL SCAASGTIFR LYDMGWYRRV SGNQRELVA SITSGGSTKY GDSVKGRFTI SRDNAKNTVY LQMSSLKPED TAVYYCNAEY RTGIWEELLD GWGQGTQVTV S SHHHHHHH H

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Macromolecule #2: Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-typ...

MacromoleculeName: Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-type opioid receptor
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.327051 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKGSADLE DNWETLNDNL KVIEKADNAA QVKDALTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLLVPRGSM VLEVSDHQVL NDAEVAALLE N FSSSYDYG ...String:
MKTIIALSYI FCLVFADYKD DDDKGSADLE DNWETLNDNL KVIEKADNAA QVKDALTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLLVPRGSM VLEVSDHQVL NDAEVAALLE N FSSSYDYG ENESDSCCTS PPCPQDFSLN FDRAFLPALY SLLFLLGLLG NGAVAAVLLS RRTALSSTDT FLLHLAVADT LL VLTLPLW AVDAAVQWVF GSGLCKVAGA LFNINFYAGA LLLACISFDR YLNIVHATQL YRRGPPARVT LTCLAVWGLC LLF ALPDFI FLSAHHDERL NATHCQYNFP QVGRTALRVL QLVAGFLLPL LVMAYCYAHI LARLKSVRLL SGSREKDRNL RRIT RLVVV VVVAFALCWT PYHLVVLVDI LMDLGALARN CGRESRVDVA KSVTSGLGYM HCCLNPLLYA FVGVKFRERM WMLLL RLGC PNQRGLQRQP SSSRRDSSWS ETS

UniProtKB: Soluble cytochrome b562, C-X-C chemokine receptor type 3, Kappa-type opioid receptor, C-X-C chemokine receptor type 3

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #5: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE

MacromoleculeName: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: LPC
Molecular weightTheoretical: 468.585 Da
Chemical component information

ChemComp-LPC:
[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE

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Macromolecule #6: N-[(1R)-1-[3-(4-ethoxyphenyl)-4-oxidanylidene-pyrido[2,3-d]pyrimi...

MacromoleculeName: 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
type: ligand / ID: 6 / Number of copies: 1 / Formula: FI6
Molecular weightTheoretical: 603.591 Da
Chemical component information

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

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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

Concentration5.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 834686
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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