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- PDB-9lz2: Cryo-EM structure of PTH1R(V2RC)-beta-arrestin1 complex -

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Basic information

Entry
Database: PDB / ID: 9lz2
TitleCryo-EM structure of PTH1R(V2RC)-beta-arrestin1 complex
Components
  • Beta-arrestin-1
  • Fab30 heavy chain
  • Fab30 light chain
  • Long-acting PTH
  • Parathyroid hormone/parathyroid hormone-related peptide receptor,Vasopressin V2 receptor
KeywordsMEMBRANE PROTEIN / Cryo-EM structure
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 / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Lysosome Vesicle Biogenesis / parathyroid hormone receptor activity / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin ...TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Lysosome Vesicle Biogenesis / parathyroid hormone receptor activity / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / clathrin heavy chain binding / Cargo recognition for clathrin-mediated endocytosis / hemostasis / telencephalon development / desensitization of G protein-coupled receptor signaling pathway / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / acetylcholine receptor binding / Class B/2 (Secretin family receptors) / G protein-coupled receptor internalization / G protein-coupled peptide receptor activity / inositol hexakisphosphate binding / osteoblast development / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / small molecule binding / positive regulation of inositol phosphate biosynthetic process / bone mineralization / phosphatidylinositol-3,4,5-trisphosphate binding / pseudopodium / positive regulation of systemic arterial blood pressure / peptide hormone binding / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / positive regulation of vasoconstriction / negative regulation of Notch signaling pathway / chondrocyte differentiation / endocytic vesicle / bone resorption / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / activation of adenylate cyclase activity / cellular response to hormone stimulus / cell maturation / response to cytokine / skeletal system development / clathrin-coated endocytic vesicle membrane / G protein-coupled receptor binding / receptor internalization / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / intracellular calcium ion homeostasis / Vasopressin regulates renal water homeostasis via Aquaporins / Cargo recognition for clathrin-mediated endocytosis / protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Clathrin-mediated endocytosis / cytoplasmic vesicle / molecular adaptor activity / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / ubiquitin-dependent protein catabolic process / basolateral plasma membrane / in utero embryonic development / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / signaling receptor complex / cell population proliferation / endosome / apical plasma membrane / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / signal transduction / protein homodimerization activity / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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. / 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
Beta-arrestin-1 / Vasopressin V2 receptor / Parathyroid hormone/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Mus musculus (house mouse)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhai, X. / Guo, J. / Shen, Q. / Chen, L. / Wang, G. / Shen, D. / Zhang, C. / Xu, X. / Mao, C. / Zhang, Y. / Liu, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of ligand-bound form of the receptor in complex with the transducer
Authors: Zhai, X. / Guo, J. / Shen, Q. / Chen, L. / Wang, G. / Shen, D. / Zhang, C. / Xu, X. / Mao, C. / Zhang, Y. / Liu, Z.
History
DepositionFeb 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Long-acting PTH
A: Beta-arrestin-1
H: Fab30 heavy chain
L: Fab30 light chain
R: Parathyroid hormone/parathyroid hormone-related peptide receptor,Vasopressin V2 receptor


Theoretical massNumber of molelcules
Total (without water)146,1305
Polymers146,1305
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Long-acting PTH


Mass: 4274.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Beta-arrestin-1 / Arrestin beta-1 / Arrestin-2


Mass: 44281.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARRB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17870
#3: Antibody Fab30 heavy chain


Mass: 17147.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Antibody Fab30 light chain


Mass: 23435.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#5: Protein Parathyroid hormone/parathyroid hormone-related peptide receptor,Vasopressin V2 receptor / PTH/PTHrP type I receptor / PTH/PTHr receptor / Parathyroid hormone 1 receptor / PTH1 receptor / ...PTH/PTHrP type I receptor / PTH/PTHr receptor / Parathyroid hormone 1 receptor / PTH1 receptor / V2R / AVPR V2 / Antidiuretic hormone receptor / Renal-type arginine vasopressin receptor


Mass: 56992.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTH1R, PTHR, PTHR1, AVPR2, ADHR, DIR, DIR3, V2R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q03431, UniProt: P30518
Has ligand of interestN
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: Cryo-EM structure of ligand-bound form of the chimeric receptor in complex with the transduce
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Bos taurus (domestic cattle)9913
31Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Spodoptera frugiperda (fall armyworm)7108
21Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 345754 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0057288
ELECTRON MICROSCOPYf_angle_d0.719895
ELECTRON MICROSCOPYf_dihedral_angle_d10.0014333
ELECTRON MICROSCOPYf_chiral_restr0.0491111
ELECTRON MICROSCOPYf_plane_restr0.0061230

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