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- EMDB-39794: Cryo-EM structure of the hGPR68-Gs complex in pH6.8 -

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Basic information

Entry
Database: EMDB / ID: EMD-39794
TitleCryo-EM structure of the hGPR68-Gs complex in pH6.8
Map data
Sample
  • Complex: Cryo-EM structure of the receptor of hGPR4-Gs complex in pH6.8
    • Protein or peptide: G-protein coupled receptor 4
KeywordspH6.8 / hGPR68 / Gs / MEMBRANE PROTEIN
Function / homology
Function and homology information


glomerular mesangial cell development / regulation of vascular permeability / response to acidic pH / Class A/1 (Rhodopsin-like receptors) / angiogenesis involved in wound healing / positive regulation of Rho protein signal transduction / regulation of cell adhesion / negative regulation of angiogenesis / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway ...glomerular mesangial cell development / regulation of vascular permeability / response to acidic pH / Class A/1 (Rhodopsin-like receptors) / angiogenesis involved in wound healing / positive regulation of Rho protein signal transduction / regulation of cell adhesion / negative regulation of angiogenesis / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of inflammatory response / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / 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-prodeshotein coupled receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhong YN / Guo LL / Yang F / Sun JP
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81773704 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the hGPR68-Gs complex in pH6.8
Authors: Zhong YN / Guo LL / Yang F / Sun JP
History
DepositionApr 18, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39794.png

Downloads & links

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Map

FileDownload / File: emd_39794.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 180 pix.
= 189.36 Å		1.05 Å/pix.
x 180 pix.
= 189.36 Å		1.05 Å/pix.
x 180 pix.
= 189.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.046279576 - 2.008323
Average (Standard dev.)0.00092752 (±0.022095498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 189.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39794_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39794_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 : Cryo-EM structure of the receptor of hGPR4-Gs complex in pH6.8

EntireName: Cryo-EM structure of the receptor of hGPR4-Gs complex in pH6.8
Components
  • Complex: Cryo-EM structure of the receptor of hGPR4-Gs complex in pH6.8
    • Protein or peptide: G-protein coupled receptor 4

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Supramolecule #1: Cryo-EM structure of the receptor of hGPR4-Gs complex in pH6.8

SupramoleculeName: Cryo-EM structure of the receptor of hGPR4-Gs complex in pH6.8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 41.026664 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGNHTWEGCH VDSRVDHLFP PSLYIFVIGV GLPTNCLALW AAYRQVQQRN ELGVYLMNLS IADLLYICTL PLWVDYFLHH DNWIHGPGS CKLFGFIFYT NIYISIAFLC CISVDRYLAV AHPLRFARLR RVKTAVAVSS VVWATELGAN SAPLFHDELF R DRYNHTFC ...String:
MGNHTWEGCH VDSRVDHLFP PSLYIFVIGV GLPTNCLALW AAYRQVQQRN ELGVYLMNLS IADLLYICTL PLWVDYFLHH DNWIHGPGS CKLFGFIFYT NIYISIAFLC CISVDRYLAV AHPLRFARLR RVKTAVAVSS VVWATELGAN SAPLFHDELF R DRYNHTFC FEKFPMEGWV AWMNLYRVFV GFLFPWALML LSYRGILRAV RGSVSTERQE KAKIKRLALS LIAIVLVCFA PY HVLLLSR SAIYLGRPWD CGFEERVFSA YHSSLAFTSL NCVADPILYC LVNEGARSDV AKALHNLLRF LASDKPQEMA NAS LTLETP LTSKRNSTAK AMTGSWAATP PSQGDQVQLK MLPPAQ

UniProtKB: G-prodeshotein 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: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.5 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282290
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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