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- EMDB-64617: Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) boun... -

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Basic information

Entry
Database: EMDB / ID: EMD-64617
TitleCryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 2 (consensus refinement)
Map dataCryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 2 (consensus refinement)
Sample
  • Complex: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin2
KeywordsG protein-coupled receptor 1 / chemerin / beta-arrestin2 / signaling protein / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCai H / Lin X / Zhao L / He M / Yu J / Zhang B / Ma Y / Xie C / Shui W / Zhao Q ...Cai H / Lin X / Zhao L / He M / Yu J / Zhang B / Ma Y / Xie C / Shui W / Zhao Q / Zhu Y / Wu B
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82121005 China
National Natural Science Foundation of China (NSFC)32401012 China
CitationJournal: Science / Year: 2025
Title: Noncanonical agonist-dependent and -independent arrestin recruitment of GPR1.
Authors: Heng Cai / Xiaowen Lin / Lechen Zhao / Maozhou He / Jie Yu / Bingjie Zhang / Yuandi Ma / Xiaohua Chang / Yuxuan Tang / Tianyu Luo / Jie Jiang / Mengna Ma / Wenqi Song / Limin Ma / Xiaojing ...Authors: Heng Cai / Xiaowen Lin / Lechen Zhao / Maozhou He / Jie Yu / Bingjie Zhang / Yuandi Ma / Xiaohua Chang / Yuxuan Tang / Tianyu Luo / Jie Jiang / Mengna Ma / Wenqi Song / Limin Ma / Xiaojing Chu / Cuiying Yi / Kun Chen / Shuo Han / Cen Xie / Wenqing Shui / Qiang Zhao / Ya Zhu / Beili Wu /
Abstract: G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors have diverse signaling properties with differential preferences for downstream pathways. Certain receptors, such as the ...G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors have diverse signaling properties with differential preferences for downstream pathways. Certain receptors, such as the chemerin receptor GPR1, undergo arrestin-mediated internalization but weak G protein signaling. However, the mechanisms of this unusual signaling pattern and its physiological relevance are unclear. We report the structures of GPR1 bound to chemerin and β-arrestin 1 or β-arrestin 2 and an agonist-free GPR1-β-arrestin 1 complex. Upon agonist stimulation, the receptor binds the two arrestins in distinct interaction patterns, which may account for their differential cellular responses. Agonist-independent internalization was mediated by an inactive, constitutively phosphorylated GPR1 that accommodates β-arrestin 1 in an unconventional pocket together with a fatty acid, which potentially provides a basis for GPR1 modulating lipid accumulation in lipid-overloaded adipocytes.
History
DepositionMay 15, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64617.png

Downloads & links

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Map

FileDownload / File: emd_64617.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 2 (consensus refinement)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.3542008 - 2.0168376
Average (Standard dev.)-0.00025648822 (±0.03929514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half 2 map of cryo-EM structure of the...

Fileemd_64617_half_map_1.map
AnnotationHalf 2 map of cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 2 (consensus refinement)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 1 map of cryo-EM structure of the...

Fileemd_64617_half_map_2.map
AnnotationHalf 1 map of cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 2 (consensus refinement)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : G protein-coupled receptor 1 in complex with chemerin and beta-ar...

EntireName: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin2
Components
  • Complex: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin2

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Supramolecule #1: G protein-coupled receptor 1 in complex with chemerin and beta-ar...

SupramoleculeName: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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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: 7.5
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: 2.1875 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123307
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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