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- EMDB-64619: Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) boun... -

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Entry
Database: EMDB / ID: EMD-64619
TitleCryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to beta-arrestin 1 in ligand-free state
Map dataCryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to beta-arrestin 1 in ligand-free state
Sample
  • Complex: G protein-coupled receptor 1 in complex with beta-arrestin1
    • Protein or peptide: Chemerin-like receptor 2,Vasopressin V2 receptor
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Nanobody 32
    • Protein or peptide: Single-chain fragment variable 30 (scFv30)
  • Ligand: PALMITOLEIC ACID
KeywordsG protein-coupled receptor 1 / chemerin / beta-arrestin1 / signaling protein / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


adipokinetic hormone binding / adipokinetic hormone receptor activity / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / hemostasis ...adipokinetic hormone binding / adipokinetic hormone receptor activity / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / hemostasis / Activation of SMO / telencephalon development / negative regulation of interleukin-8 production / arrestin family protein binding / G protein-coupled receptor internalization / neuropeptide binding / Lysosome Vesicle Biogenesis / : / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / positive regulation of vasoconstriction / pseudopodium / positive regulation of systemic arterial blood pressure / negative regulation of interleukin-6 production / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / endocytic vesicle / enzyme inhibitor activity / neuropeptide signaling pathway / activation of adenylate cyclase activity / cellular response to hormone stimulus / insulin-like growth factor receptor binding / response to cytokine / clathrin-coated pit / negative regulation of protein ubiquitination / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / cytoplasmic vesicle membrane / clathrin-coated endocytic vesicle membrane / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / G protein-coupled receptor binding / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / Vasopressin regulates renal water homeostasis via Aquaporins / Cargo recognition for clathrin-mediated endocytosis / glucose homeostasis / protein transport / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / endosome / neuron projection / Ub-specific processing proteases / nuclear body / protein ubiquitination / G protein-coupled receptor signaling pathway / Golgi membrane / negative regulation of cell population proliferation / lysosomal membrane / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / chromatin / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Chemerin-like receptor 2 / Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Formyl peptide receptor-related / Arrestin-like, N-terminal / Arrestin C-terminal-like domain ...Chemerin-like receptor 2 / Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Formyl peptide receptor-related / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / 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. / Immunoglobulin E-set
Similarity search - Domain/homology
Vasopressin V2 receptor / Chemerin-like receptor 2 / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia phage EcSzw-2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_64619.png

Downloads & links

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Map

FileDownload / File: emd_64619.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 beta-arrestin 1 in ligand-free state
Projections & slices

Image control

Size
Brightness
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-2.349471 - 3.551532
Average (Standard dev.)-0.000028759154 (±0.053498983)
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: #1

Fileemd_64619_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_64619_half_map_2.map
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Histogram (log scale)

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Sample components

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Entire : G protein-coupled receptor 1 in complex with beta-arrestin1

EntireName: G protein-coupled receptor 1 in complex with beta-arrestin1
Components
  • Complex: G protein-coupled receptor 1 in complex with beta-arrestin1
    • Protein or peptide: Chemerin-like receptor 2,Vasopressin V2 receptor
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Nanobody 32
    • Protein or peptide: Single-chain fragment variable 30 (scFv30)
  • Ligand: PALMITOLEIC ACID

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Supramolecule #1: G protein-coupled receptor 1 in complex with beta-arrestin1

SupramoleculeName: G protein-coupled receptor 1 in complex with beta-arrestin1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Chemerin-like receptor 2,Vasopressin V2 receptor

MacromoleculeName: Chemerin-like receptor 2,Vasopressin V2 receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.035852 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFAGSWS HPQFEKGSGA GASAGSWSHP QFEKGSDYKD DDDKEFLEVL FQGPEDLEET LFEEFENYSY DLDYYSLES DLEEKVQLGV VHWVSLVLYC LAFVLGIPGN AIVIWFTGFK WKKTVTTLWF LNLAIADFIF LLFLPLYISY V AMNFHWPF ...String:
MKTIIALSYI FCLVFAGSWS HPQFEKGSGA GASAGSWSHP QFEKGSDYKD DDDKEFLEVL FQGPEDLEET LFEEFENYSY DLDYYSLES DLEEKVQLGV VHWVSLVLYC LAFVLGIPGN AIVIWFTGFK WKKTVTTLWF LNLAIADFIF LLFLPLYISY V AMNFHWPF GIWLCKANSF TAQLNMFASV FFLTVISLDH YIHLIHPCLS HRHRTLKNSL IVIIFIWLLA SLIGGPALYF RD TVEFNNH TLCYNNFQKH DPDLTLIRHH VLTWVKFIIG YLFPLLTMSI CYLCLIFKVK KRSILISSRH FWTILVVVVA FVV CWTPYH LFSIWELTIH HNSYSHHVMQ AGIPLSTGLA FLNSCLNPIL YVLISKKFQA RFRSSVAEIA RGRTPPSLGP QDE (SEP)C(TPO)(TPO)A(SEP) (SEP)(SEP)LAKDTSS

UniProtKB: Chemerin-like receptor 2, Vasopressin V2 receptor

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Macromolecule #2: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.107105 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTAA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA IGVDYEVKAF VAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTAA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA IGVDYEVKAF VAENLEEKIH K RNSVRLVI EKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD IVLFNTA QCKVPVAMEE ADDTVAPSST FSKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP ENETPVDTNL

UniProtKB: Beta-arrestin-1

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Macromolecule #3: Nanobody 32

MacromoleculeName: Nanobody 32 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage EcSzw-2 (virus)
Molecular weightTheoretical: 13.238716 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCVVSGFFFD TVTMAWYRRA PGKHRELVAS ATAGGTTTYA DSVKDRFTIS RDNAKNTVYL QMNSLKPED TAVYYCNTFV RSLSWGQGTQ VTVSSHHHHH H

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Macromolecule #4: Single-chain fragment variable 30 (scFv30)

MacromoleculeName: Single-chain fragment variable 30 (scFv30) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.157861 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKG TTAASGSSGG SSSGAEVQLV ESGGGLVQPG GSLRLSCAAS GFNVYSSSIH W VRQAPGKG ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKG TTAASGSSGG SSSGAEVQLV ESGGGLVQPG GSLRLSCAAS GFNVYSSSIH W VRQAPGKG LEWVASISSY YGYTYYADSV KGRFTISADT SKNTAYLQMN SLRAEDTAVY YCARSRQFWY SGLDYWGQGT LV TVSSA

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Macromolecule #5: PALMITOLEIC ACID

MacromoleculeName: PALMITOLEIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PAM
Molecular weightTheoretical: 254.408 Da
Chemical component information

ChemComp-PAM:
PALMITOLEIC ACID

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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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 413367
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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