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- PDB-23cy: Cryo-EM structure of the MRGPRX4-miniGsq complex bound to the inv... -

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Basic information

Entry
Database: PDB / ID: 23cy
TitleCryo-EM structure of the MRGPRX4-miniGsq complex bound to the inverse agonist cmpd54-4, local
ComponentsSoluble cytochrome b562,Mas-related G-protein coupled receptor member X4
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


G protein-coupled bile acid receptor activity / sensory perception of itch / electron transport chain / G protein-coupled receptor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / electron transfer activity / periplasmic space / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / plasma membrane
Similarity search - Function
Mas-related G protein-coupled receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / Soluble cytochrome b562 / Mas-related G protein-coupled receptor member X4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsCao, C. / Wang, C. / Zhang, M. / Ji, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2025YFA1309100 China
National Natural Science Foundation of China (NSFC)82504820 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the MRGPRX4-miniGsq complex bound to the inverse agonist cmpd54-4, local
Authors: Zhang, M.
History
DepositionFeb 1, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7982
Polymers53,3961
Non-polymers4021
Water00
1


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

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Components

#1: Protein Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4 / Cytochrome b-562 / Sensory neuron-specific G-protein coupled receptor 5/6


Mass: 53396.020 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, MRGPRX4, MRGX4, SNSR5, SNSR6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: Q96LA9
#2: Chemical ChemComp-A1E43 / (2~{S})-2-[[3-[[2-chloranyl-4-(trifluoromethyl)phenoxy]methyl]phenyl]carbonylamino]propanoic acid


Mass: 401.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15ClF3NO4 / Feature type: SUBJECT OF INVESTIGATION
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: GPCR bound with a ligand / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.053 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
9PHENIX1.21.2model refinement
13cryoSPARC4.4.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 432382 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 47.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00581952
ELECTRON MICROSCOPYf_angle_d0.70932669
ELECTRON MICROSCOPYf_chiral_restr0.0419336
ELECTRON MICROSCOPYf_plane_restr0.0058310
ELECTRON MICROSCOPYf_dihedral_angle_d19.6351669

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