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- PDB-7s8l: CryoEM structure of Gq-coupled MRGPRX2 with peptide agonist Corti... -

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Basic information

Entry
Database: PDB / ID: 7s8l
TitleCryoEM structure of Gq-coupled MRGPRX2 with peptide agonist Cortistatin-14
Components
  • (Guanine nucleotide-binding protein ...) x 2
  • Cortistatin 14
  • Gs-mini-Gq chimera
  • Mas-related G-protein coupled receptor member X2
  • scFv16
KeywordsSIGNALING PROTEIN / GPCR
Function / homology
Function and homology information


mast cell secretagogue receptor activity / mast cell activation / neuropeptide binding / mast cell degranulation / sleep / Olfactory Signaling Pathway / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through PLC beta / positive regulation of cytokinesis ...mast cell secretagogue receptor activity / mast cell activation / neuropeptide binding / mast cell degranulation / sleep / Olfactory Signaling Pathway / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through PLC beta / positive regulation of cytokinesis / Activation of the phototransduction cascade / ADP signalling through P2Y purinoceptor 12 / Prostacyclin signalling through prostacyclin receptor / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G protein-coupled acetylcholine receptor signaling pathway / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon signaling in metabolic regulation / cardiac muscle cell apoptotic process / G beta:gamma signalling through CDC42 / sensory perception of taste / alkylglycerophosphoethanolamine phosphodiesterase activity / G alpha (z) signalling events / G-protein beta/gamma-subunit complex / rhodopsin mediated signaling pathway / cellular response to catecholamine stimulus / G beta:gamma signalling through BTK / G-protein gamma-subunit binding / Glucagon-type ligand receptors / positive regulation of potassium ion transmembrane transport / Vasopressin regulates renal water homeostasis via Aquaporins / adenylate cyclase-activating dopamine receptor signaling pathway / photoreceptor disc membrane / photoreceptor outer segment membrane / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / spectrin binding / G-protein beta-subunit binding / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / ADP signalling through P2Y purinoceptor 1 / G protein-coupled receptor activity / Wnt signaling pathway, calcium modulating pathway / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events / ADORA2B mediated anti-inflammatory cytokines production / extracellular vesicle / sensory perception of pain / phospholipase C-activating G protein-coupled receptor signaling pathway / GTPase binding / retina development in camera-type eye / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / photoreceptor inner segment / G alpha (s) signalling events / G alpha (i) signalling events / G alpha (q) signalling events / negative regulation of inflammatory response to antigenic stimulus / cell population proliferation / cell body / Ras protein signal transduction / Extra-nuclear estrogen signaling / lysosomal membrane / cellular response to hypoxia / positive regulation of cytosolic calcium ion concentration / platelet activation / protein folding / GTPase activity / G protein-coupled receptor signaling pathway / synapse / dendrite / protein-containing complex binding / signal transduction / extracellular exosome / membrane / integral component of membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mas-related G protein-coupled receptor family / Mas-related G protein-coupled receptor X1/X2 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit ...Mas-related G protein-coupled receptor family / Mas-related G protein-coupled receptor X1/X2 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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) / : / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Mas-related G-protein coupled receptor member X2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsCao, C. / Fay, J.F. / Gumpper, R.H. / Roth, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nature / Year: 2021
Title: Structure, function and pharmacology of human itch GPCRs.
Authors: Can Cao / Hye Jin Kang / Isha Singh / He Chen / Chengwei Zhang / Wenlei Ye / Byron W Hayes / Jing Liu / Ryan H Gumpper / Brian J Bender / Samuel T Slocum / Brian E Krumm / Katherine Lansu / ...Authors: Can Cao / Hye Jin Kang / Isha Singh / He Chen / Chengwei Zhang / Wenlei Ye / Byron W Hayes / Jing Liu / Ryan H Gumpper / Brian J Bender / Samuel T Slocum / Brian E Krumm / Katherine Lansu / John D McCorvy / Wesley K Kroeze / Justin G English / Jeffrey F DiBerto / Reid H J Olsen / Xi-Ping Huang / Shicheng Zhang / Yongfeng Liu / Kuglae Kim / Joel Karpiak / Lily Y Jan / Soman N Abraham / Jian Jin / Brian K Shoichet / Jonathan F Fay / Bryan L Roth /
Abstract: The MRGPRX family of receptors (MRGPRX1-4) is a family of mas-related G-protein-coupled receptors that have evolved relatively recently. Of these, MRGPRX2 and MRGPRX4 are key physiological and ...The MRGPRX family of receptors (MRGPRX1-4) is a family of mas-related G-protein-coupled receptors that have evolved relatively recently. Of these, MRGPRX2 and MRGPRX4 are key physiological and pathological mediators of itch and related mast cell-mediated hypersensitivity reactions. MRGPRX2 couples to both G and G in mast cells. Here we describe agonist-stabilized structures of MRGPRX2 coupled to G and G in ternary complexes with the endogenous peptide cortistatin-14 and with a synthetic agonist probe, respectively, and the development of potent antagonist probes for MRGPRX2. We also describe a specific MRGPRX4 agonist and the structure of this agonist in a complex with MRGPRX4 and G. Together, these findings should accelerate the structure-guided discovery of therapeutic agents for pain, itch and mast cell-mediated hypersensitivity.
History
DepositionSep 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
R: Mas-related G-protein coupled receptor member X2
A: Cortistatin 14
B: Gs-mini-Gq chimera
C: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
D: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
E: scFv16


Theoretical massNumber of molelcules
Total (without water)139,9576
Polymers139,9576
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, C1
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10680 Å2
ΔGint-76 kcal/mol
Surface area49410 Å2

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Components

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Protein , 2 types, 2 molecules RB

#1: Protein Mas-related G-protein coupled receptor member X2


Mass: 37146.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRGPRX2, MRGX2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96LB1
#3: Protein Gs-mini-Gq chimera


Mass: 28084.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

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Guanine nucleotide-binding protein ... , 2 types, 2 molecules CD

#4: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37728.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873
#5: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768

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Protein/peptide / Antibody , 2 types, 2 molecules AE

#2: Protein/peptide Cortistatin 14


Mass: 1726.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: Antibody scFv16


Mass: 27409.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)

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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: MRGPRX2-Gq Cortistatin-14 / Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Molecular weightValue: 150 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Trichoplusia ni (cabbage looper)7111
31Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2029927 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038353
ELECTRON MICROSCOPYf_angle_d0.5511373
ELECTRON MICROSCOPYf_dihedral_angle_d18.1592805
ELECTRON MICROSCOPYf_chiral_restr0.0421329
ELECTRON MICROSCOPYf_plane_restr0.0031430

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