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- EMDB-81097: Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-81097
TitleCryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex
Map data
Sample
  • Complex: Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30H
    • Protein or peptide: Fab30L
    • Protein or peptide: Pituitary adenylate cyclase-activating polypeptide type I receptor
    • Protein or peptide: Pituitary adenylate cyclase-activating polypeptide 27
  • Ligand: water
KeywordsGPCR / Beta arrestin1 / MEMBRANE PROTEIN/IMMUNE SYSTEM / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhao L / Yuan Q / Zhang M
Funding support China, 1 items
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, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_81097.png

Downloads & links

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Map

FileDownload / File: emd_81097.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.348
Minimum - Maximum-1.171374 - 3.2132878
Average (Standard dev.)0.011382877 (±0.03887059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 321.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex

EntireName: Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex
Components
  • Complex: Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30H
    • Protein or peptide: Fab30L
    • Protein or peptide: Pituitary adenylate cyclase-activating polypeptide type I receptor
    • Protein or peptide: Pituitary adenylate cyclase-activating polypeptide 27
  • Ligand: water

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Supramolecule #1: Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex

SupramoleculeName: Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #5, #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.985207 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKGTRVFKKA SPNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTCAFR YGREDLDVLG LTFRKDLFVA NVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPCSVTLQP GPEDTGKACG VDYEVKAFCA ENLEEKIHKR N SVRLVIRK ...String:
MKGTRVFKKA SPNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTCAFR YGREDLDVLG LTFRKDLFVA NVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPCSVTLQP GPEDTGKACG VDYEVKAFCA ENLEEKIHKR N SVRLVIRK VQYAPERPGP QPTAETTRQF LMSDKPLHLE ASLDKEIYYH GEPISVNVHV TNNTNKTVKK IKISVRQYAD IC LFNTAQY KCPVAMEEAD DTVAPSSTFC KVYTLTPFLC NNREKRGLAL DGKLKHEDTN LASSTLLREG ANREILGIIV SYK VKVKLV VSRGGLLGDL ASSDVAVELP FTLMHPKPKE EPPHREVPEN ETPVDTNLIE LDTNDDDAAA EDFAR

UniProtKB: Beta-arrestin-1

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Macromolecule #2: Fab30H

MacromoleculeName: Fab30H / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.584467 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEISEVQLVE SGGGLVQPGG SLRLSCAASG FNVYSSSIHW VRQAPGKGLE WVASISSYYC YTYYADSVKG RFTISADTSK NTAYLQMNS LRAEDTAVYY CARSRQFWYS GLDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
MEISEVQLVE SGGGLVQPGG SLRLSCAASG FNVYSSSIHW VRQAPGKGLE WVASISSYYC YTYYADSVKG RFTISADTSK NTAYLQMNS LRAEDTAVYY CARSRQFWYS GLDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD KT

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Macromolecule #3: Fab30L

MacromoleculeName: Fab30L / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #4: Pituitary adenylate cyclase-activating polypeptide 27

MacromoleculeName: Pituitary adenylate cyclase-activating polypeptide 27 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.15265 KDa
SequenceString:
HSDGIFTDSY SRYRKQMAVK KYLAAVL(NH2)

UniProtKB: Pituitary adenylate cyclase-activating polypeptide

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Macromolecule #5: Pituitary adenylate cyclase-activating polypeptide type I receptor

MacromoleculeName: Pituitary adenylate cyclase-activating polypeptide type I receptor
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.349129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHSDCIFKKE QAMCLEKIQR ANELMGFNDS SPGCPGMWDN ITCWKPAHVG EMVLVSCPEL FRIFNPDQVW ETETIGESDF GDSNSLDLS DMGVVSRNCT EDGWSEPFPH YFDACGFDEY ESETGDQDYY YLSVKALYTV GYSTSLVTLT TAMVILCRFR K LHCTRNFI ...String:
MHSDCIFKKE QAMCLEKIQR ANELMGFNDS SPGCPGMWDN ITCWKPAHVG EMVLVSCPEL FRIFNPDQVW ETETIGESDF GDSNSLDLS DMGVVSRNCT EDGWSEPFPH YFDACGFDEY ESETGDQDYY YLSVKALYTV GYSTSLVTLT TAMVILCRFR K LHCTRNFI HMNLFVSFML RAISVFIKDW ILYAEQDSNH CFISTVECKA VMVFFHYCVV SNYFWLFIEG LYLFTLLVET FF PERRYFY WYTIIGWGTP TVCVTVWATL RLYFDDTGCW DMNDSTALWW VIKGPVVGSI MVNFVLFIGI IVILVQKLQS PDM GGNESS IYLRLARSTL LLIPLFGIHY TVFAFSPENV SKRERLVFEL GLGSFQGFVV AVLYCFLNGE VQAEIKRKWR SWKV NRYFA VDFKHRHPSA RGRTPPSLGP QDESC(TPO)(TPO)A(SEP)(SEP) (SEP)LAKDTSS

UniProtKB: Pituitary adenylate cyclase-activating polypeptide type I receptor

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.04
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 18.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 104393
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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