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- EMDB-68872: Cryo-EM structure of the MRGPRX4-miniGsq complex bound to the ago... -

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Basic information

Entry
Database: EMDB / ID: EMD-68872
TitleCryo-EM structure of the MRGPRX4-miniGsq complex bound to the agonist dexamethasone phosphate (DEX-P),local
Map data
Sample
  • Complex: GPCR bound with a ligand
    • Protein or peptide: Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4
  • Ligand: (11alpha,16alpha)-9-fluoro-11,17-dihydroxy-16-methyl-3,20-dioxopregna-1,4-dien-21-yl dihydrogen phosphate
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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsCao C / Wang C / Zhang M / Ji Z
Funding support China, 2 items
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 agonist dexamethasone phosphate (DEX-P),local
Authors: Zhang M
History
DepositionFeb 1, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68872.png

Downloads & links

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Map

FileDownload / File: emd_68872.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 356 pix.
= 291.92 Å		0.82 Å/pix.
x 356 pix.
= 291.92 Å		0.82 Å/pix.
x 356 pix.
= 291.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.6778939 - 1.0985575
Average (Standard dev.)-0.000047337795 (±0.00952549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 291.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68872_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68872_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPCR bound with a ligand

EntireName: GPCR bound with a ligand
Components
  • Complex: GPCR bound with a ligand
    • Protein or peptide: Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4
  • Ligand: (11alpha,16alpha)-9-fluoro-11,17-dihydroxy-16-methyl-3,20-dioxopregna-1,4-dien-21-yl dihydrogen phosphate

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Supramolecule #1: GPCR bound with a ligand

SupramoleculeName: GPCR bound with a ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53 KDa

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Macromolecule #1: Soluble cytochrome b562,Mas-related G-protein coupled receptor me...

MacromoleculeName: Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.39602 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAKL QTMHHHHHHH HHHENLYFQG GTTMADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LGSTLEVLFQ GPDPTVPVFG T KLTPINGR ...String:
DYKDDDDAKL QTMHHHHHHH HHHENLYFQG GTTMADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LGSTLEVLFQ GPDPTVPVFG T KLTPINGR EETPCYNQTL SFTVLTCIIS LVGLTGNAVV LWLLGYRMRR NAVSIYILNL AAADFLFLSF QIIRSPLRLI NI SHLIRKI LVSVMTFPYF TGLSMLSAIS TERCLSVLWP IWYRCRRPTH LSAVVCVLLW GLSLLFSMLE WRFCDFLFSG ADS SWCETS DFIPVAWLIF LCVVLCVSSL VLLVRILCGS RKMPLTRLYV TILLTVLVFL LCGLPFGILG ALIYRMHLNL EVLY CHVYL VCMSLSSLNS SANPIIYFFV GSFRQRQNRQ NLKLVLQRAL QDKPEVDKGE GQLPEESLEL SGSRLGP

UniProtKB: Soluble cytochrome b562, Mas-related G protein-coupled receptor member X4

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Macromolecule #2: (11alpha,16alpha)-9-fluoro-11,17-dihydroxy-16-methyl-3,20-dioxopr...

MacromoleculeName: (11alpha,16alpha)-9-fluoro-11,17-dihydroxy-16-methyl-3,20-dioxopregna-1,4-dien-21-yl dihydrogen phosphate
type: ligand / ID: 2 / Number of copies: 1 / Formula: 3T5
Molecular weightTheoretical: 472.441 Da
Chemical component information

ChemComp-3T5:
(11alpha,16alpha)-9-fluoro-11,17-dihydroxy-16-methyl-3,20-dioxopregna-1,4-dien-21-yl dihydrogen phosphate

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8yrg

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 174116
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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