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- EMDB-64618: Composite map of the G protein-coupled receptor 1 (GPR1) bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-64618
TitleComposite map of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 2
Map dataCryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 2
Sample
  • Complex: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin2
    • Protein or peptide: Retinoic acid receptor responder protein 2
    • Protein or peptide: Nanobody 32
    • Protein or peptide: Single-chain fragment variable 30 (scFv30)
    • Protein or peptide: Beta-arrestin-2,Beta-arrestin-1
    • Protein or peptide: Chemerin-like receptor 2,Vasopressin V2 receptor
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsG protein-coupled receptor 1 / chemerin / beta-arrestin 2 / signaling protein / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


postsynaptic signal transduction / positive regulation of synaptic transmission, dopaminergic / adipokinetic hormone binding / adipokinetic hormone receptor activity / platelet dense granule lumen / 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 ...postsynaptic signal transduction / positive regulation of synaptic transmission, dopaminergic / adipokinetic hormone binding / adipokinetic hormone receptor activity / platelet dense granule lumen / 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 / positive regulation of cardiac muscle cell differentiation / WNT5A-dependent internalization of FZD4 / protein kinase B binding / regulation of lipid catabolic process / antifungal innate immune response / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / negative regulation of toll-like receptor signaling pathway / hemostasis / desensitization of G protein-coupled receptor signaling pathway / Activation of SMO / telencephalon development / embryonic digestive tract development / antifungal humoral response / response to caloric restriction / negative regulation of interleukin-8 production / negative regulation of interleukin-12 production / positive regulation of chemotaxis / arrestin family protein binding / negative regulation of natural killer cell mediated cytotoxicity / G protein-coupled receptor internalization / neuropeptide binding / adult walking behavior / negative regulation of interleukin-1 beta production / Lysosome Vesicle Biogenesis / G protein-coupled dopamine receptor signaling pathway / : / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / positive regulation of vasoconstriction / positive regulation of macrophage chemotaxis / 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 tumor necrosis factor production / negative regulation of Notch signaling pathway / endocytic vesicle / enzyme inhibitor activity / D1 dopamine receptor binding / positive regulation of fat cell differentiation / neuropeptide signaling pathway / retinoid metabolic process / activation of adenylate cyclase activity / cellular response to hormone stimulus / insulin-like growth factor receptor binding / clathrin-coated pit / response to cytokine / negative regulation of canonical NF-kappaB signal transduction / extracellular matrix / negative regulation of protein ubiquitination / transforming growth factor beta receptor signaling pathway / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / cytoplasmic vesicle membrane / response to activity / cell chemotaxis / excitatory postsynaptic potential / 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 / receptor internalization / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / chemotaxis / 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 / Signaling by BRAF and RAF1 fusions / endocytic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / insulin receptor signaling pathway / Platelet degranulation / 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 / defense response to Gram-negative bacterium / G alpha (s) signalling events
Similarity search - Function
Chemerin-like receptor 2 / Retinoic acid receptor responder protein 2 / Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Formyl peptide receptor-related / Arrestin-like, N-terminal ...Chemerin-like receptor 2 / Retinoic acid receptor responder protein 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 / Cystatin superfamily / 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) / Immunoglobulin E-set
Similarity search - Domain/homology
Vasopressin V2 receptor / Beta-arrestin-2 / Chemerin-like receptor 2 / Beta-arrestin-1 / Retinoic acid receptor responder protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia phage EcSzw-2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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_64618.png

Downloads & links

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Map

FileDownload / File: emd_64618.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
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: 0.19
Minimum - Maximum-1.1090516 - 2.396503
Average (Standard dev.)0.0091756005 (±0.043335244)
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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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
    • Protein or peptide: Retinoic acid receptor responder protein 2
    • Protein or peptide: Nanobody 32
    • Protein or peptide: Single-chain fragment variable 30 (scFv30)
    • Protein or peptide: Beta-arrestin-2,Beta-arrestin-1
    • Protein or peptide: Chemerin-like receptor 2,Vasopressin V2 receptor
  • Ligand: CHOLESTEROL HEMISUCCINATE

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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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Macromolecule #1: Retinoic acid receptor responder protein 2

MacromoleculeName: Retinoic acid receptor responder protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.720475 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MKTIIALSYI FCLVFAELTE AQRRGLQVAL EEFHKHPPVQ WAFQETSVES AVDTPFPAGI FVRLEFKLQQ TSCRKRDWKK PECKVRPNG RKRKCLACIK LGSEDKVLGR LVHCPIETQV LREAEEHQET QCLRVQRAGE DPHSFYFPGQ FAFS

UniProtKB: Retinoic acid receptor responder protein 2

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Macromolecule #2: Nanobody 32

MacromoleculeName: Nanobody 32 / type: protein_or_peptide / ID: 2 / 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 #3: Single-chain fragment variable 30 (scFv30)

MacromoleculeName: Single-chain fragment variable 30 (scFv30) / type: protein_or_peptide / ID: 3 / 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 #4: Beta-arrestin-2,Beta-arrestin-1

MacromoleculeName: Beta-arrestin-2,Beta-arrestin-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.50848 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGEKPGTRVF KKSSPNGKLT VYLGKRDFVD HLDKVDPVDG VVLVDPDYLK DRKVFVTLTV AFRYGREDLD VLGLSFRKDL FIATYQAFP PVPNPPRPPT RLQDRLLRKL GQHAHPFFFT IPQNLPSSVT LQPGPEDTGK ALGVDFEIRA FVAKSLEEKS H KRNSVRLV ...String:
MGEKPGTRVF KKSSPNGKLT VYLGKRDFVD HLDKVDPVDG VVLVDPDYLK DRKVFVTLTV AFRYGREDLD VLGLSFRKDL FIATYQAFP PVPNPPRPPT RLQDRLLRKL GQHAHPFFFT IPQNLPSSVT LQPGPEDTGK ALGVDFEIRA FVAKSLEEKS H KRNSVRLV IRKVQFAPEK PGPQPSAETT RHFLMSDRSL HLEASLDKEL YYHGEPLNVN VHVTNNSTKT VKKIKVSVRQ YA DIVLFST AQYKVPVAQL EQDDQVSPSS TFSKVYTITP LLSDNREKRG LALDGKLKHE DTNLASSTIV KEGANKEVLG ILV SYRVKV KLVVSRGGDV SVELPFVLMH PKPKEEPPHR EVPENETPVD TNL

UniProtKB: Beta-arrestin-2, Beta-arrestin-1

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Macromolecule #5: Chemerin-like receptor 2,Vasopressin V2 receptor

MacromoleculeName: Chemerin-like receptor 2,Vasopressin V2 receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.03184 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 YIHLIHPVLS 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 #6: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 3.5 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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