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- PDB-9uym: Composite map of the G protein-coupled receptor 1 (GPR1) bound to... -

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Basic information

Entry
Database: PDB / ID: 9uym
TitleComposite map of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 2
Components
  • Beta-arrestin-2,Beta-arrestin-1
  • Chemerin-like receptor 2,Vasopressin V2 receptor
  • Nanobody 32
  • Retinoic acid receptor responder protein 2
  • Single-chain fragment variable 30 (scFv30)
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / G protein-coupled receptor 1 / chemerin / beta-arrestin 2 / signaling protein / 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 / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / platelet dense granule lumen / 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 / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / platelet dense granule lumen / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / positive regulation of cardiac muscle cell differentiation / protein kinase B binding / WNT5A-dependent internalization of FZD4 / regulation of lipid catabolic process / antifungal innate immune response / angiotensin receptor binding / hemostasis / TGFBR3 regulates TGF-beta signaling / desensitization of G protein-coupled receptor signaling pathway / negative regulation of toll-like 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 / G protein-coupled receptor internalization / arrestin family protein binding / negative regulation of natural killer cell mediated cytotoxicity / neuropeptide binding / adult walking behavior / G protein-coupled dopamine receptor signaling pathway / negative regulation of interleukin-1 beta production / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / positive regulation of macrophage chemotaxis / positive regulation of vasoconstriction / positive regulation of Rho protein signal transduction / 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 / endocytic vesicle / negative regulation of Notch signaling pathway / enzyme inhibitor activity / neuropeptide signaling pathway / D1 dopamine receptor binding / positive regulation of fat cell differentiation / 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 protein ubiquitination / negative regulation of canonical NF-kappaB signal transduction / extracellular matrix / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transforming growth factor beta receptor signaling pathway / GTPase activator activity / cytoplasmic vesicle membrane / Activated NOTCH1 Transmits Signal to the Nucleus / response to activity / cell chemotaxis / excitatory postsynaptic potential / clathrin-coated endocytic vesicle membrane / Signaling by high-kinase activity BRAF mutants / G protein-coupled receptor binding / G protein-coupled receptor activity / MAP2K and MAPK activation / receptor internalization / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / chemotaxis / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / Signaling by BRAF and RAF1 fusions / 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 / Formyl peptide receptor-related / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal ...Chemerin-like receptor 2 / Retinoic acid receptor responder protein 2 / Vasopressin V2 receptor / Vasopressin receptor / Formyl peptide receptor-related / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / 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
CHOLESTEROL HEMISUCCINATE / 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)
MethodELECTRON MICROSCOPY / single 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, 2items
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: Cai, H. / Lin, X. / Zhao, L. / He, M. / Yu, J. / Zhang, B. / Ma, Y. / Chang, X. / Tang, Y. / Luo, T. / Jiang, J. / Ma, M. / Song, W. / Ma, L. / Chu, X. / Yi, C. / Chen, K. / Han, S. / Xie, C. ...Authors: Cai, H. / Lin, X. / Zhao, L. / He, M. / Yu, J. / Zhang, B. / Ma, Y. / Chang, X. / Tang, Y. / Luo, T. / Jiang, J. / Ma, M. / Song, W. / Ma, L. / Chu, X. / Yi, C. / Chen, K. / Han, S. / Xie, C. / Shui, W. / Zhao, Q. / Zhu, Y. / Wu, B.
History
DepositionMay 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Retinoic acid receptor responder protein 2
B: Nanobody 32
C: Single-chain fragment variable 30 (scFv30)
A: Beta-arrestin-2,Beta-arrestin-1
R: Chemerin-like receptor 2,Vasopressin V2 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,1446
Polymers146,6575
Non-polymers4871
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 3 molecules LAR

#1: Protein Retinoic acid receptor responder protein 2 / Chemerin / RAR-responsive protein TIG2 / Tazarotene-induced gene 2 protein


Mass: 17720.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARRES2, TIG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99969
#4: Protein Beta-arrestin-2,Beta-arrestin-1 / Arrestin beta-2 / Non-visual arrestin-3 / Arrestin beta-1 / Non-visual arrestin-2


Mass: 41508.480 Da / Num. of mol.: 1 / Mutation: C17G,C60V,C126S,C141L,C151V,C243V,C252V and C270S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARRB2, ARB2, ARR2, ARRB1, ARR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32121, UniProt: P49407
#5: Protein Chemerin-like receptor 2,Vasopressin V2 receptor / Chemerin chemokine-like receptor 2 / Chemokine-like receptor 2 / G-protein coupled receptor 1 / V2R ...Chemerin chemokine-like receptor 2 / Chemokine-like receptor 2 / G-protein coupled receptor 1 / V2R / AVPR V2 / Antidiuretic hormone receptor / Renal-type arginine vasopressin receptor


Mass: 48031.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CMKLR2, GPR1, AVPR2, ADHR, DIR, DIR3, V2R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P46091, UniProt: P30518

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Antibody , 2 types, 2 molecules BC

#2: Antibody Nanobody 32


Mass: 13238.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage EcSzw-2 (virus) / Production host: Escherichia coli BL21 (bacteria)
#3: Antibody Single-chain fragment variable 30 (scFv30)


Mass: 26157.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin2
Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 2.1875 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123307 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037768
ELECTRON MICROSCOPYf_angle_d0.62510625
ELECTRON MICROSCOPYf_dihedral_angle_d13.0952531
ELECTRON MICROSCOPYf_chiral_restr0.041265
ELECTRON MICROSCOPYf_plane_restr0.0041300

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