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- PDB-7jqd: Crystal Structure of PAC1r in complex with peptide antagonist -

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Basic information

Entry
Database: PDB / ID: 7jqd
TitleCrystal Structure of PAC1r in complex with peptide antagonist
Components
  • Peptide-43
  • Pituitary adenylate cyclase-activating polypeptide type I receptor
KeywordsSIGNALING PROTEIN/ANTAGONIST / ECD / Complex / Antagonist / GPCR / SIGNALING PROTEIN-ANTAGONIST complex
Function / homology
Function and homology information


negative regulation of response to reactive oxygen species / development of primary female sexual characteristics / vasoactive intestinal polypeptide receptor activity / positive regulation of cAMP-mediated signaling / NGF-independant TRKA activation / neuropeptide binding / G protein-coupled peptide receptor activity / positive regulation of small GTPase mediated signal transduction / positive regulation of inositol phosphate biosynthetic process / positive regulation of calcium ion transport into cytosol ...negative regulation of response to reactive oxygen species / development of primary female sexual characteristics / vasoactive intestinal polypeptide receptor activity / positive regulation of cAMP-mediated signaling / NGF-independant TRKA activation / neuropeptide binding / G protein-coupled peptide receptor activity / positive regulation of small GTPase mediated signal transduction / positive regulation of inositol phosphate biosynthetic process / positive regulation of calcium ion transport into cytosol / peptide hormone binding / adenylate cyclase binding / bicellular tight junction / multicellular organismal response to stress / cAMP-mediated signaling / caveola / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / small GTPase binding / Glucagon-type ligand receptors / response to estradiol / signaling receptor activity / G alpha (s) signalling events / spermatogenesis / response to ethanol / cell surface receptor signaling pathway / cell differentiation / receptor complex / endosome / response to xenobiotic stimulus / intracellular membrane-bounded organelle / cell surface / plasma membrane
Similarity search - Function
GPCR, family 2, pituitary adenylate cyclase activating polypeptide type 1 receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / 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 ...GPCR, family 2, pituitary adenylate cyclase activating polypeptide type 1 receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / 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.
Similarity search - Domain/homology
Pituitary adenylate cyclase-activating polypeptide type I receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lutzomyia longipalpis (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPiper, D.E. / Hu, E. / Fang-Tsao, H.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of Selective Pituitary Adenylate Cyclase 1 Receptor (PAC1R) Antagonist Peptides Potent in a Maxadilan/PACAP38-Induced Increase in Blood Flow Pharmacodynamic Model.
Authors: Hu, E. / Hong, F.T. / Aral, J. / Long, J. / Piper, D.E. / Poppe, L. / Andrews, K.L. / Hager, T. / Davis, C. / Li, H. / Wong, P. / Gavva, N. / Shi, L. / Zhu, D.X.D. / Lehto, S.G. / Xu, C. / Miranda, L.P.
History
DepositionAug 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pituitary adenylate cyclase-activating polypeptide type I receptor
B: Peptide-43


Theoretical massNumber of molelcules
Total (without water)16,2482
Polymers16,2482
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Activity assays
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-13 kcal/mol
Surface area7520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.680, 67.680, 56.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Pituitary adenylate cyclase-activating polypeptide type I receptor / PACAP-R1


Mass: 11858.230 Da / Num. of mol.: 1 / Fragment: UNP residues 18-143 / Mutation: A18G, P19S, A20M, M21A, C25G, del(89-109)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADCYAP1R1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41586
#2: Protein/peptide Peptide-43


Mass: 4390.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lutzomyia longipalpis (insect)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 20% PEG3000, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationMonochromator: single crystal cylindrically bent Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.7→29.1 Å / Num. obs: 3871 / % possible obs: 98.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 45.67 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.098 / Rrim(I) all: 0.234 / Net I/σ(I): 5.4 / Num. measured all: 20415 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.835.30.96326925080.7260.4451.0651.899.9
8.95-29.14.30.1255481280.9860.0650.1419.195.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIXdev-2328_1692refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JOD

2jod


Resolution: 2.7→29.096 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2915 397 10.29 %
Rwork0.2037 3462 -
obs0.2125 3859 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.18 Å2 / Biso mean: 47.2662 Å2 / Biso min: 25.87 Å2
Refinement stepCycle: final / Resolution: 2.7→29.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 8 984
Biso mean---37.84 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091006
X-RAY DIFFRACTIONf_angle_d0.9381354
X-RAY DIFFRACTIONf_chiral_restr0.049132
X-RAY DIFFRACTIONf_plane_restr0.006176
X-RAY DIFFRACTIONf_dihedral_angle_d18.956611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7001-3.09040.32641410.2439111399
3.0904-3.89210.31871140.2061114498
3.8921-29.0960.26291420.1894120598

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