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- EMDB-61840: Cryo-EM structure of the receptor of xGPR4-apo in pH8.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-61840
TitleCryo-EM structure of the receptor of xGPR4-apo in pH8.0
Map data
Sample
  • Complex: Cryo-EM structure of the receptor of xGPR4-apo in pH8.0
    • Protein or peptide: G-protein coupled receptor 4
KeywordspH8.0 / xGPR4 / receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


response to acidic pH / G protein-coupled receptor activity / plasma membrane
Similarity search - Function
G protein-coupled receptor 4 orphan / 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
G-protein coupled receptor 4
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsRong NK / Wen X / Yang F / Sun JP
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81773704 China
CitationJournal: Cell / Year: 2025
Title: Evolutionary study and structural basis of proton sensing by Mus GPR4 and Xenopus GPR4.
Authors: Xin Wen / Pan Shang / Haidi Chen / Lulu Guo / Naikang Rong / Xiaoyu Jiang / Xuan Li / Junyan Liu / Gongming Yang / Jiacheng Zhang / Kongkai Zhu / Qingbiao Meng / Xuefei He / Zhihai Wang / ...Authors: Xin Wen / Pan Shang / Haidi Chen / Lulu Guo / Naikang Rong / Xiaoyu Jiang / Xuan Li / Junyan Liu / Gongming Yang / Jiacheng Zhang / Kongkai Zhu / Qingbiao Meng / Xuefei He / Zhihai Wang / Zili Liu / Haoran Cheng / Yilin Zheng / Bifei Zhang / Jiaojiao Pang / Zhaoqian Liu / Peng Xiao / Yuguo Chen / Lunxu Liu / Fengming Luo / Xiao Yu / Fan Yi / Pengju Zhang / Fan Yang / Cheng Deng / Jin-Peng Sun /
Abstract: Animals have evolved pH-sensing membrane receptors, such as G-protein-coupled receptor 4 (GPR4), to monitor pH changes related to their physiology and generate adaptive reactions. However, the ...Animals have evolved pH-sensing membrane receptors, such as G-protein-coupled receptor 4 (GPR4), to monitor pH changes related to their physiology and generate adaptive reactions. However, the evolutionary trajectory and structural mechanism of proton sensing by GPR4 remain unresolved. Here, we observed a positive correlation between the optimal pH of GPR4 activity and the blood pH range across different species. By solving 7-cryoelectron microscopy (cryo-EM) structures of Xenopus tropicalis GPR4 (xtGPR4) and Mus musculus GPR4 (mmGPR4) under varying pH conditions, we identified that protonation of H and H enabled polar network establishment and tighter association between the extracellular loop 2 (ECL2) and 7 transmembrane (7TM) domain, as well as a conserved propagating path, which are common mechanisms underlying protonation-induced GPR4 activation across different species. Moreover, protonation of distinct extracellular H contributed to the more acidic optimal pH range of xtGPR4. Overall, our study revealed common and distinct mechanisms of proton sensing by GPR4, from a structural, functional, and evolutionary perspective.
History
DepositionOct 9, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61840.png

Downloads & links

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Map

FileDownload / File: emd_61840.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.009684435 - 2.2162666
Average (Standard dev.)0.0003676109 (±0.014995158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61840_msk_1.map
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Half map: #2

Fileemd_61840_half_map_1.map
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Half map: #1

Fileemd_61840_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of the receptor of xGPR4-apo in pH8.0

EntireName: Cryo-EM structure of the receptor of xGPR4-apo in pH8.0
Components
  • Complex: Cryo-EM structure of the receptor of xGPR4-apo in pH8.0
    • Protein or peptide: G-protein coupled receptor 4

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Supramolecule #1: Cryo-EM structure of the receptor of xGPR4-apo in pH8.0

SupramoleculeName: Cryo-EM structure of the receptor of xGPR4-apo in pH8.0
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)

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Macromolecule #1: G-protein coupled receptor 4

MacromoleculeName: G-protein coupled receptor 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Molecular weightTheoretical: 38.083359 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSNFTPDACN VDSGLDSVLP PSLYALVFTL GLPANLLALW AAWLQVRKGR ELGVYLLNLS LSDLLLICAL PPWTDYYLRR DVWGYGPGA CRLFGFVFYT NLYVGAAFLS CVSADRYLAV AHPLRFPGAR PIRSAAAVSA LIWMLELAAN APPLLGEAIH R DRYNHTFC ...String:
MSNFTPDACN VDSGLDSVLP PSLYALVFTL GLPANLLALW AAWLQVRKGR ELGVYLLNLS LSDLLLICAL PPWTDYYLRR DVWGYGPGA CRLFGFVFYT NLYVGAAFLS CVSADRYLAV AHPLRFPGAR PIRSAAAVSA LIWMLELAAN APPLLGEAIH R DRYNHTFC YESYPLSGRG AALANVGRVL AGFLLPWGVM MLCYAGLLRA LRGSASCEQR ERRRVRRLAL GLPCVALLCY GP YHALLLL RSLVFLVGGG SVDAGGGCAL EERLFPAYHA SLALATLNCL ADPALYCLAC PGARGEVAKV VGGVVAWAMG KER RAWGER GGNGRGCGEG EEVGMVELRG NGREFVV

UniProtKB: G-protein coupled receptor 4

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.875 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
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: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184326
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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