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- PDB-27em: Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex -

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Basic information

Entry
Database: PDB / ID: 27em
TitleCryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex
Components
  • (Pituitary adenylate cyclase-activating polypeptide ...) x 2
  • Beta-arrestin-1
  • Fab30H
  • Fab30L
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / GPCR / Beta arrestin1 / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


pituitary adenylate cyclase activating polypeptide activity / development of primary female sexual characteristics / type 1 vasoactive intestinal polypeptide receptor binding / type 2 vasoactive intestinal polypeptide receptor binding / pituitary adenylate cyclase-activating polypeptide receptor activity / vasoactive intestinal polypeptide receptor activity / angiotensin receptor binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of growth hormone secretion / TGFBR3 regulates TGF-beta signaling ...pituitary adenylate cyclase activating polypeptide activity / development of primary female sexual characteristics / type 1 vasoactive intestinal polypeptide receptor binding / type 2 vasoactive intestinal polypeptide receptor binding / pituitary adenylate cyclase-activating polypeptide receptor activity / vasoactive intestinal polypeptide receptor activity / angiotensin receptor binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of growth hormone secretion / TGFBR3 regulates TGF-beta signaling / regulation of cellular response to oxidative stress / Activation of SMO / negative regulation of interleukin-8 production / positive regulation of small GTPase mediated signal transduction / neuropeptide hormone activity / desensitization of G protein-coupled receptor signaling pathway / NGF-independant TRKA activation / insulin secretion / arrestin family protein binding / cAMP biosynthetic process / G protein-coupled peptide receptor activity / G protein-coupled receptor internalization / stress fiber assembly / positive regulation of cAMP/PKA signal transduction / negative regulation of Notch signaling pathway / positive regulation of cardiac muscle hypertrophy / sensory perception / negative regulation of interleukin-6 production / Lysosome Vesicle Biogenesis / peptide hormone receptor binding / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / positive regulation of protein kinase activity / positive regulation of inositol phosphate biosynthetic process / pseudopodium / peptide hormone binding / positive regulation of calcium ion transport into cytosol / adenylate cyclase binding / positive regulation of receptor internalization / multicellular organismal response to stress / positive regulation of GTPase activity / bicellular tight junction / activation of adenylate cyclase activity / insulin-like growth factor receptor binding / negative regulation of protein ubiquitination / clathrin-coated pit / intracellular glucose homeostasis / GTPase activator activity / regulation of G protein-coupled receptor signaling pathway / cytoplasmic vesicle membrane / enzyme inhibitor activity / negative regulation of canonical NF-kappaB signal transduction / Activated NOTCH1 Transmits Signal to the Nucleus / female pregnancy / neuropeptide signaling pathway / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein phosphorylation / caveola / G protein-coupled receptor binding / small GTPase binding / neuron projection development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / protein transport / 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 / Signaling by BRAF and RAF1 fusions / response to estradiol / Glucagon-type ligand receptors / regulation of protein localization / cell-cell signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / Clathrin-mediated endocytosis / signaling receptor activity / positive regulation of cytosolic calcium ion concentration / Thrombin signalling through proteinase activated receptors (PARs) / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytoplasmic vesicle / spermatogenesis / ubiquitin-dependent protein catabolic process / cell differentiation / G alpha (s) signalling events / molecular adaptor activity / response to ethanol / proteasome-mediated ubiquitin-dependent protein catabolic process / perikaryon / positive regulation of ERK1 and ERK2 cascade / transcription coactivator activity / cell surface receptor signaling pathway / signaling receptor complex / endosome / neuron projection / response to xenobiotic stimulus / protein ubiquitination / Ub-specific processing proteases / signaling receptor binding
Similarity search - Function
GPCR, family 2, pituitary adenylate cyclase activating polypeptide type 1 receptor / : / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal ...GPCR, family 2, pituitary adenylate cyclase activating polypeptide type 1 receptor / : / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / 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. / Immunoglobulin E-set
Similarity search - Domain/homology
Pituitary adenylate cyclase-activating polypeptide / Pituitary adenylate cyclase-activating polypeptide type I receptor / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhao, L. / Yuan, Q. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Pharmacol Sin / Year: 2026
Title: Structural basis of β-arrestin coupling and transducer selectivity in PAC1R.
Authors: Min Zhang / Xin Li / Qing-Ning Yuan / Wen Hu / H Eric Xu / Li-Hua Zhao /
Abstract: The pituitary adenylate cyclase-activating polypeptide receptor (PAC1R) is a class B G protein-coupled receptor (GPCR) that engages both G proteins and β-arrestins to mediate diverse signaling ...The pituitary adenylate cyclase-activating polypeptide receptor (PAC1R) is a class B G protein-coupled receptor (GPCR) that engages both G proteins and β-arrestins to mediate diverse signaling responses, yet how PAC1R adopts distinct intracellular conformations to achieve this transducer selectivity remains poorly understood. Here, we report the cryo-electron microscopy structure of PAC1R in complex with β-arrestin 1 (βarr1), revealing a core-engaged conformation. Comparison with the G-bound PAC1R structure shows that βarr1 engagement is associated with remodeling of the intracellular transmembrane bundle, including TM5 reorientation and inward movement of TM6, resulting in a receptor core geometry distinct from that of the G protein-bound state. Comparison with the βarr1-bound parathyroid hormone receptor 1 (PTH1R) structure further reveals both conserved and receptor-specific features of βarr1 engagement. Although outward displacement of the TM5 cytoplasmic end is observed in both PAC1R-βarr1 and PTH1R-βarr1 complexes, its specific direction and the resulting TM5-TM6 rearrangements differ between receptors, correlating with distinct βarr1 finger loop orientations within the receptor core. Together, these findings suggest that β-arrestin core engagement by class B GPCRs is accompanied by receptor-specific intracellular remodeling that may contribute to transducer selectivity in PAC1R.
History
DepositionMay 28, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Beta-arrestin-1
C: Fab30H
E: Fab30L
P: Pituitary adenylate cyclase-activating polypeptide 27
R: Pituitary adenylate cyclase-activating polypeptide type I receptor


Theoretical massNumber of molelcules
Total (without water)146,5075
Polymers146,5075
Non-polymers00
Water181
1


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

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Components

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Pituitary adenylate cyclase-activating polypeptide ... , 2 types, 2 molecules PR

#4: Protein/peptide Pituitary adenylate cyclase-activating polypeptide 27 / PACAP-27 / PACAP27


Mass: 3152.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18509
#5: Protein Pituitary adenylate cyclase-activating polypeptide type I receptor / PAC1 receptor / PAC1R / PACAP type I receptor / PACAP-R-1 / PACAP-R1


Mass: 51349.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADCYAP1R1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41586

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Antibody , 2 types, 2 molecules CE

#2: Antibody Fab30H


Mass: 24584.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody Fab30L


Mass: 23435.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm)

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Protein / Non-polymers , 2 types, 2 molecules B

#1: Protein Beta-arrestin-1 / Arrestin beta-1 / Non-visual arrestin-2


Mass: 43985.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARRB1, ARR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P49407
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex
Type: COMPLEX / Entity ID: #1-#3, #5, #4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.04
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 18000 nm / Nominal defocus min: 8000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104393 / Symmetry type: POINT

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