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- EMDB-63521: Cryo-EM structure of PTH1R(V2RC)-beta-arrestin1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63521
TitleCryo-EM structure of PTH1R(V2RC)-beta-arrestin1 complex
Map data
Sample
  • Complex: Cryo-EM structure of ligand-bound form of the chimeric receptor in complex with the transduce
    • Protein or peptide: Long-acting PTH
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain
    • Protein or peptide: Parathyroid hormone/parathyroid hormone-related peptide receptor,Vasopressin V2 receptor
KeywordsCryo-EM structure / MEMBRANE PROTEIN
Function / homology
Function and homology information


TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / renal water retention / Lysosome Vesicle Biogenesis / parathyroid hormone receptor activity / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / regulation of systemic arterial blood pressure by vasopressin / Vasopressin-like receptors ...TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / renal water retention / Lysosome Vesicle Biogenesis / parathyroid hormone receptor activity / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / regulation of systemic arterial blood pressure by vasopressin / Vasopressin-like receptors / renal water absorption / vasopressin receptor activity / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / Cargo recognition for clathrin-mediated endocytosis / clathrin heavy chain binding / telencephalon development / hemostasis / protein localization to non-motile cilium / Clathrin-mediated endocytosis / desensitization of G protein-coupled receptor signaling pathway / acetylcholine receptor binding / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / clathrin-dependent endocytosis / G protein-coupled receptor internalization / inositol hexakisphosphate binding / negative regulation of Notch signaling pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / sensory perception / clathrin binding / small molecule binding / positive regulation of systemic arterial blood pressure / positive regulation of inositol phosphate biosynthetic process / pseudopodium / positive regulation of intracellular signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / peptide hormone binding / positive regulation of smoothened signaling pathway / positive regulation of receptor internalization / skeletal system development / positive regulation of vasoconstriction / endocytic vesicle / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cellular response to hormone stimulus / activation of adenylate cyclase activity / clathrin-coated endocytic vesicle membrane / receptor internalization / positive regulation of protein phosphorylation / G protein-coupled receptor binding / intracellular calcium ion homeostasis / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / basolateral plasma membrane / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / signaling receptor complex / endosome / apical plasma membrane / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / endoplasmic reticulum / protein homodimerization activity / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vasopressin V2 receptor / GPCR, family 2, parathyroid hormone receptor / Vasopressin receptor / 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 ...Vasopressin V2 receptor / GPCR, family 2, parathyroid hormone receptor / Vasopressin receptor / 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 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / G-protein coupled receptors family 1 signature. / Immunoglobulin E-set / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Beta-arrestin-1 / Vasopressin V2 receptor / Parathyroid hormone/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others) / Bos taurus (domestic cattle) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhai X / Guo J / Shen Q / Chen L / Wang G / Shen D / Zhang C / Xu X / Mao C / Zhang Y / Liu Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Core conformation of arrestin coupling to parathyroid hormone type 1 receptor.
Authors: Xiuwen Zhai / Jia Guo / Qingya Shen / Li-Nan Chen / Gang Wang / Dan-Dan Shen / Changming Zhang / Xiaodong Xu / Chunyou Mao / Yan Zhang / Zhihong Liu /
Abstract: The recruitment of β-arrestin (βarr) by G-protein-coupled receptor (GPCR) holds imperative importance in physiological processes, while the mechanisms underlying arrestin engagement with receptors ...The recruitment of β-arrestin (βarr) by G-protein-coupled receptor (GPCR) holds imperative importance in physiological processes, while the mechanisms underlying arrestin engagement with receptors remain obscure. The parathyroid hormone type 1 receptor (PTH1R), as a prototypical class B1 receptor, incorporates arrestin for signaling and regulates G-protein signaling by distinct mechanisms. Here, we report three cryo-electron microscopy structures of β-arrestin1 (βarr1) engaged with the activated wild-type and chimeric PTH1R in core conformation, revealing a distinctive binding mode of βarr1 coupling to PTH1R compared to other GPCRs. In addition to the pronounced kinking of transmembrane (TM) 6, βarr1 establishes extensive interactions with the core cavity of PTH1R by promoting the outward movement of TM5 and intracellular loop (ICL) 2, stabilizing the core conformation of the complex. Further, our work shows that the core coupling mode of βarr with PTH1R mediates receptor internalization and trafficking. Collectively, our work offers a paradigm for the arrestin coupling to class B1 GPCR and regulating the signaling transduction.
History
DepositionFeb 21, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63521.png

Downloads & links

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Map

FileDownload / File: emd_63521.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum0.0 - 2.4477048
Average (Standard dev.)0.0007163576 (±0.021149006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63521_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_63521_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of ligand-bound form of the chimeric receptor i...

EntireName: Cryo-EM structure of ligand-bound form of the chimeric receptor in complex with the transduce
Components
  • Complex: Cryo-EM structure of ligand-bound form of the chimeric receptor in complex with the transduce
    • Protein or peptide: Long-acting PTH
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain
    • Protein or peptide: Parathyroid hormone/parathyroid hormone-related peptide receptor,Vasopressin V2 receptor

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Supramolecule #1: Cryo-EM structure of ligand-bound form of the chimeric receptor i...

SupramoleculeName: Cryo-EM structure of ligand-bound form of the chimeric receptor in complex with the transduce
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Long-acting PTH

MacromoleculeName: Long-acting PTH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.274027 KDa
SequenceString:
AVAEIQLMHQ RAKWIQDARR RAFLHKLIAE IHTAEI

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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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 44.281496 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVEPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVEPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI EKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD ICLFNTA QYKCPVAMEE ADDTVAPSST FCKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP EHETPVDTNL IELDTNDDDI VFEDFAR

UniProtKB: Beta-arrestin-1

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Macromolecule #3: Fab30 heavy chain

MacromoleculeName: Fab30 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 17.14702 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V

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Macromolecule #4: Fab30 light chain

MacromoleculeName: Fab30 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #5: Parathyroid hormone/parathyroid hormone-related peptide receptor,...

MacromoleculeName: Parathyroid hormone/parathyroid hormone-related peptide receptor,Vasopressin V2 receptor
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.992648 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DADDVMTKEE QIFLLHRAQA QCEKRLKEVL QRPASIMESD KGWTSASTSG KPRKDKASGK LYPESEEDKE APTGSRYRGR PCLPEWDHI LCWPLGAPGE VVAVPCPDYI YDFNHKGHAY RRCDRNGSWE LVPGHNRTWA NYSECVKFLT NETREREVFD R LAMIYTVG ...String:
DADDVMTKEE QIFLLHRAQA QCEKRLKEVL QRPASIMESD KGWTSASTSG KPRKDKASGK LYPESEEDKE APTGSRYRGR PCLPEWDHI LCWPLGAPGE VVAVPCPDYI YDFNHKGHAY RRCDRNGSWE LVPGHNRTWA NYSECVKFLT NETREREVFD R LAMIYTVG YSVSLASLTV AVLILAYFRR LHCTRNYIHM HLFLSFMLRA VSIFVKDAVL YSGATLDEAE RLTEEELRAI AQ APPPPAT AAAGYAGCRV AVTFFLYFLA TNYYWILVEG LYLHSLIFMA FFSEKKYLWG FTVFGWGLPA VFVAVWVSVR ATL ANTGCW DLSSGNKKWI IQVPILASIV LNFILFINIV RVLATKLRET NAGRCDTRQQ YRKLLKSTLV LMPLFGVHYI VFMA TPYTE VSGTLWQVQM HYEMLFNSFQ GFFVAIIYCF CNGEVQAEIK KSWSRWTLAL DFKRKARSGG GGSGGGSGGA RGREP PELG PQDE(SEP)C(TPO)(TPO)A(SEP) (SEP)(SEP)LAKD

UniProtKB: Parathyroid hormone/parathyroid hormone-related peptide receptor, Vasopressin V2 receptor

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Frames/image: 1-40 / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6nbi

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 345754
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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