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- EMDB-39749: Cryo-EM structure of the receptor of hGPR68-Gs complex in pH6.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-39749
TitleCryo-EM structure of the receptor of hGPR68-Gs complex in pH6.0
Map data
Sample
  • Complex: Cryo-EM structure of the receptor of hGPR68-Gs complex in pH6.0
    • Protein or peptide: Ovarian cancer G-protein coupled receptor 1
KeywordspH6.0 / hGPR68 / MEMBRANE PROTE / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of osteoclast development / cellular response to pH / negative regulation of monocyte differentiation / osteoclast development / Class A/1 (Rhodopsin-like receptors) / insulin secretion / monocyte differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / G protein-coupled receptor activity / G alpha (q) signalling events ...positive regulation of osteoclast development / cellular response to pH / negative regulation of monocyte differentiation / osteoclast development / Class A/1 (Rhodopsin-like receptors) / insulin secretion / monocyte differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / G protein-coupled receptor activity / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / inflammatory response / plasma membrane
Similarity search - Function
OGR1 sphingosylphosphorylcholine receptor / 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
Ovarian cancer G-protein coupled receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhong YN / Guo LL
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 receptor of hGPR68-Gs complex in pH6.0
Authors: Zhong YN / Guo LL
History
DepositionApr 15, 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_39749.png

Downloads & links

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Map

FileDownload / File: emd_39749.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.028593859 - 2.724518
Average (Standard dev.)0.00095803227 (±0.018575318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 222.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39749_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39749_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_39749_half_map_2.map
Projections & Slices
AxesZYX

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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 hGPR68-Gs complex in pH6.0

EntireName: Cryo-EM structure of the receptor of hGPR68-Gs complex in pH6.0
Components
  • Complex: Cryo-EM structure of the receptor of hGPR68-Gs complex in pH6.0
    • Protein or peptide: Ovarian cancer G-protein coupled receptor 1

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Supramolecule #1: Cryo-EM structure of the receptor of hGPR68-Gs complex in pH6.0

SupramoleculeName: Cryo-EM structure of the receptor of hGPR68-Gs complex in pH6.0
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ovarian cancer G-protein coupled receptor 1

MacromoleculeName: Ovarian cancer G-protein coupled receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.511469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGNITADNSS MSCTIDHTIH QTLAPVVYVT VLVVGFPANC LSLYFGYLQI KARNELGVYL CNLTVADLFY ICSLPFWLQY VLQHDNWSH GDLSCQVCGI LLYENIYISV GFLCCISVDR YLAVAHPFRF HQFRTLKAAV GVSVVIWAKE LLTSIYFLMH E EVIEDENQ ...String:
MGNITADNSS MSCTIDHTIH QTLAPVVYVT VLVVGFPANC LSLYFGYLQI KARNELGVYL CNLTVADLFY ICSLPFWLQY VLQHDNWSH GDLSCQVCGI LLYENIYISV GFLCCISVDR YLAVAHPFRF HQFRTLKAAV GVSVVIWAKE LLTSIYFLMH E EVIEDENQ HRVCFEHYPI QAWQRAINYY RFLVGFLFPI CLLLASYQGI LRAVRRSHGT QKSRKDQIQR LVLSTVVIFL AC FLPYHVL LLVRSVWEAS CDFAKGVFNA YHFSLLLTSF NCVADPVLYC FVSETTHRDL ARLRGACLAF LTCSRTGRAR EA

UniProtKB: Ovarian cancer G-protein coupled receptor 1

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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
VitrificationCryogen name: ETHANE-PROPANE

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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: 1.8 µm / Nominal defocus min: 1.2 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134460
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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