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Yorodumi- EMDB-36233: CryoEM structure of Gi-coupled MRGPRX1 with peptide agonist BAM8-22 -
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Basic information
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| Title | CryoEM structure of Gi-coupled MRGPRX1 with peptide agonist BAM8-22 | |||||||||
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Keywords | itch receptor / Mas-related GPCRs / MRGPRX1 / STRUCTURAL PROTEIN | |||||||||
| Function / homology | Function and homology informationsynaptic vesicle lumen / general adaptation syndrome, behavioral process / response to chloroquine / chromaffin granule lumen / sneeze reflex / opioid peptide activity / opioid receptor binding / positive regulation of behavioral fear response / negative regulation of sensory perception of pain / neuronal dense core vesicle lumen ...synaptic vesicle lumen / general adaptation syndrome, behavioral process / response to chloroquine / chromaffin granule lumen / sneeze reflex / opioid peptide activity / opioid receptor binding / positive regulation of behavioral fear response / negative regulation of sensory perception of pain / neuronal dense core vesicle lumen / synaptic signaling via neuropeptide / response to epinephrine / response to peptide / symmetric synapse / sensory perception of itch / cell body fiber / cellular response to vitamin D / drinking behavior / G protein-coupled opioid receptor signaling pathway / neuropeptide hormone activity / behavioral response to ethanol / C-C chemokine receptor activity / sensory perception / response to immobilization stress / transmission of nerve impulse / locomotory exploration behavior / cellular response to transforming growth factor beta stimulus / glial cell proliferation / regulation of eating behavior / adenylate cyclase inhibitor activity / T cell migration / positive regulation of protein localization to cell cortex / positive regulation of relaxation of smooth muscle / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / cellular response to cAMP / axon terminus / acute-phase response / cellular response to forskolin / regulation of mitotic spindle organization / Peptide ligand-binding receptors / mast cell degranulation / chemokine-mediated signaling pathway / response to nicotine / Post-translational protein phosphorylation / neuropeptide signaling pathway / Regulation of insulin secretion / cellular response to virus / response to prostaglandin E / response to calcium ion / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / response to toxic substance / response to peptide hormone / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / osteoblast differentiation / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / response to estradiol / GDP binding / G beta:gamma signalling through BTK / photoreceptor disc membrane / ADP signalling through P2Y purinoceptor 12 / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / transmembrane signaling receptor activity / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / cell migration / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Sun JP / Xu HE / Yang F / Liu ZM / Guo LL / Zhang YM / Fang GX / Tie L / Zhuang YM / Xue CY | |||||||||
| Funding support | China, 2 items
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Citation | Journal: Nat Commun / Year: 2023Title: Ligand recognition and G protein coupling of the human itch receptor MRGPRX1. Authors: Lulu Guo / Yumu Zhang / Guoxing Fang / Lu Tie / Yuming Zhuang / Chenyang Xue / Qi Liu / Minghui Zhang / Kongkai Zhu / Chongzhao You / Peiyu Xu / Qingning Yuan / Chao Zhang / Lei Liu / ...Authors: Lulu Guo / Yumu Zhang / Guoxing Fang / Lu Tie / Yuming Zhuang / Chenyang Xue / Qi Liu / Minghui Zhang / Kongkai Zhu / Chongzhao You / Peiyu Xu / Qingning Yuan / Chao Zhang / Lei Liu / Naikang Rong / Shengxuan Peng / Yuan Liu / Chuanzheng Wang / Xin Luo / Zongyao Lv / Dongwei Kang / Xiao Yu / Cheng Zhang / Yi Jiang / Xinzhong Dong / Jiuyao Zhou / Zhongmin Liu / Fan Yang / H Eric Xu / Jin-Peng Sun / ![]() Abstract: MRGPRX1, a Mas-related GPCR (MRGPR), is a key receptor for itch perception and targeting MRGPRX1 may have potential to treat both chronic itch and pain. Here we report cryo-EM structures of the ...MRGPRX1, a Mas-related GPCR (MRGPR), is a key receptor for itch perception and targeting MRGPRX1 may have potential to treat both chronic itch and pain. Here we report cryo-EM structures of the MRGPRX1-Gi1 and MRGPRX1-Gq trimers in complex with two peptide ligands, BAM8-22 and CNF-Tx2. These structures reveal a shallow orthosteric pocket and its conformational plasticity for sensing multiple different peptidic itch allergens. Distinct from MRGPRX2, MRGPRX1 contains a unique pocket feature at the extracellular ends of TM3 and TM4 to accommodate the peptide C-terminal "RF/RY" motif, which could serve as key mechanisms for peptidic allergen recognition. Below the ligand binding pocket, the GXPFGXF/W motif is essential for the inward tilting of the upper end of TM6 to induce receptor activation. Moreover, structural features inside the ligand pocket and on the cytoplasmic side of MRGPRX1 are identified as key elements for both Gi and Gq signaling. Collectively, our studies provide structural insights into understanding itch sensation, MRGPRX1 activation, and downstream G protein signaling. | |||||||||
| History |
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_36233.map.gz | 33 MB | EMDB map data format | |
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| Header (meta data) | emd-36233-v30.xml emd-36233.xml | 21 KB 21 KB | Display Display | EMDB header |
| Images | emd_36233.png | 89.2 KB | ||
| Filedesc metadata | emd-36233.cif.gz | 6.6 KB | ||
| Others | emd_36233_half_map_1.map.gz emd_36233_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36233 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36233 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8jggMC ![]() 8jgbC ![]() 8jgfC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_36233.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.89 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_36233_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_36233_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
-Entire : CryoEM structure of Gi-coupled MRGPRX1 with peptide agonist BAM8-22
| Entire | Name: CryoEM structure of Gi-coupled MRGPRX1 with peptide agonist BAM8-22 |
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| Components |
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-Supramolecule #1: CryoEM structure of Gi-coupled MRGPRX1 with peptide agonist BAM8-22
| Supramolecule | Name: CryoEM structure of Gi-coupled MRGPRX1 with peptide agonist BAM8-22 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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| Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
| Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 6.633625 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFREK UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #2: BAM8-22
| Macromolecule | Name: BAM8-22 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 1.603797 KDa |
| Sequence | String: PEWWMDYQKR Y UniProtKB: Proenkephalin-A |
-Macromolecule #3: Single-Chain Fragment Variable 16
| Macromolecule | Name: Single-Chain Fragment Variable 16 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 30.363043 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSAG G GGSGGGGS ...String: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSAG G GGSGGGGS GGGGSADIVM TQATSSVPVT PGESVSISCR SSKSLLHSNG NTYLYWFLQR PGQSPQLLIY RMSNLASGVP DR FSGSGSG TAFTLTISRL EAEDVGVYYC MQHLEYPLTF GAGTKLEL |
-Macromolecule #4: Guanine nucleotide-binding protein G(i) subunit alpha-1
| Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-1 type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 40.415031 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGGQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCA TDTKNVQFVF DAVTDVIIKN NLKDCGLF UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1 |
-Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
| Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 38.561152 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: LEVLFQGPCG SSGSELDQLR QEAEQLKNQI RDARKACADA TLSQITNNID PVGRIQMRTR RTLRGHLAKI YAMHWGTDSR LLVSASQDG KLIIWDSYTT NKVHAIPLRS SWVMTCAYAP SGNYVACGGL DNICSIYNLK TREGNVRVSR ELAGHTGYLS C CRFLDDNQ ...String: LEVLFQGPCG SSGSELDQLR QEAEQLKNQI RDARKACADA TLSQITNNID PVGRIQMRTR RTLRGHLAKI YAMHWGTDSR LLVSASQDG KLIIWDSYTT NKVHAIPLRS SWVMTCAYAP SGNYVACGGL DNICSIYNLK TREGNVRVSR ELAGHTGYLS C CRFLDDNQ IVTSSGDTTC ALWDIETGQQ TTTFTGHTGD VMSLSLAPDT RLFVSGACDA SAKLWDVREG MCRQTFTGHE SD INAICFF PNGNAFATGS DDATCRLFDL RADQELMTYS HDNIICGITS VSFSKSGRLL LAGYDDFNCN VWDALKADRA GVL AGHDNR VSCLGVTDDG MAVATGSWDS FLKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #6: Mas-related G-protein coupled receptor member X1
| Macromolecule | Name: Mas-related G-protein coupled receptor member X1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 36.276906 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MDPTISTLDT ELTPINGTEE TLCYKQTLSL TVLTCIVSLV GLTGNAVVLW LLGCRMRRNA FSIYILNLAA ADFLFLSGRL IYSLLSFIS IPHTISKILY PVMMFSYFAG LSFLSAVSTE RCLSVLWPIW YRCHRPTHLS AVVCVLLWAL SLLRSILEWM L CGFLFSGA ...String: MDPTISTLDT ELTPINGTEE TLCYKQTLSL TVLTCIVSLV GLTGNAVVLW LLGCRMRRNA FSIYILNLAA ADFLFLSGRL IYSLLSFIS IPHTISKILY PVMMFSYFAG LSFLSAVSTE RCLSVLWPIW YRCHRPTHLS AVVCVLLWAL SLLRSILEWM L CGFLFSGA DSAWCQTSDF ITVAWLIFLC VVLCGSSLVL LIRILCGSRK IPLTRLYVTI LLTVLVFLLC GLPFGIQFFL FL WIHVDRE VLFCHVHLVS IFLSALNSSA NPIIYFFVGS FRQRQNRQNL KLVLQRALQD ASEVDEGGGQ LPEEILELSG SRL EQ UniProtKB: Mas-related G protein-coupled receptor member X1 |
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
| Startup model | Type of model: OTHER |
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| Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 924644 |
| Initial angle assignment | Type: ANGULAR RECONSTITUTION |
| Final angle assignment | Type: ANGULAR RECONSTITUTION |
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Keywords
Homo sapiens (human)
Authors
China, 2 items
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Y (Row.)
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FIELD EMISSION GUN
