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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 / hemostasis / TGFBR3 regulates TGF-beta signaling ...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 / hemostasis / TGFBR3 regulates TGF-beta signaling / Activation of SMO / telencephalon development / negative regulation of interleukin-8 production / G protein-coupled receptor internalization / arrestin family protein binding / neuropeptide binding / 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 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 / endocytic vesicle / negative regulation of Notch signaling pathway / enzyme inhibitor activity / neuropeptide signaling pathway / 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 / GTPase activator activity / cytoplasmic vesicle membrane / Activated NOTCH1 Transmits Signal to the Nucleus / 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 / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / Signaling by BRAF and RAF1 fusions / 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 / neuron projection / endosome / Ub-specific processing proteases / protein ubiquitination / nuclear body / 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 / cytoplasm / cytosol
Similarity search - Function
Chemerin-like receptor 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 ...Chemerin-like receptor 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 / 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 / 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: 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, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 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
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: 0.27
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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64619_half_map_2.map
Projections & Slices
AxesZYX

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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 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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