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- PDB-1gea: RECEPTOR-BOUND CONFORMATION OF PACAP21 -

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Basic information

Entry
Database: PDB / ID: 1gea
TitleRECEPTOR-BOUND CONFORMATION OF PACAP21
ComponentsPITUITARY ADENYLATE CYCLASE ACTIVATING POLYPEPTIDEPituitary adenylate cyclase-activating peptide
KeywordsNEUROPEPTIDE / BETA COIL / CONSECUTIVE BETA TURNS / TYPE-II BETA TURN / TYPE-I BETA TURN / HELIX
Function / homology
Function and homology information


pituitary adenylate cyclase activating polypeptide activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of growth hormone secretion / NGF-independant TRKA activation / neuropeptide hormone activity / regulation of G protein-coupled receptor signaling pathway / insulin secretion / peptide hormone receptor binding / cAMP-mediated signaling / negative regulation of cell cycle ...pituitary adenylate cyclase activating polypeptide activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of growth hormone secretion / NGF-independant TRKA activation / neuropeptide hormone activity / regulation of G protein-coupled receptor signaling pathway / insulin secretion / peptide hormone receptor binding / cAMP-mediated signaling / negative regulation of cell cycle / neuropeptide signaling pathway / positive regulation of protein kinase activity / activation of adenylate cyclase activity / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / positive regulation of GTPase activity / neuron projection development / regulation of protein localization / cell-cell signaling / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / perikaryon / G alpha (s) signalling events / positive regulation of ERK1 and ERK2 cascade / neuron projection / signaling receptor binding / positive regulation of transcription by RNA polymerase II / extracellular region
Similarity search - Function
: / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
Pituitary adenylate cyclase-activating polypeptide
Similarity search - Component
MethodSOLUTION NMR / Iterative relaxation matrix analysis (IRMA), simulated annealing (SA)
AuthorsInooka, H. / Ohtaki, T. / Kitahara, O. / Ikegami, T. / Endo, S. / Kitada, C. / Ogi, K. / Onda, H. / Fujino, M. / Shirakawa, M.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Conformation of a peptide ligand bound to its G-protein coupled receptor.
Authors: Inooka, H. / Ohtaki, T. / Kitahara, O. / Ikegami, T. / Endo, S. / Kitada, C. / Ogi, K. / Onda, H. / Fujino, M. / Shirakawa, M.
History
DepositionOct 20, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PITUITARY ADENYLATE CYCLASE ACTIVATING POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)2,5231
Polymers2,5231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200structures with the lowest energy
RepresentativeModel #12closest to the average

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Components

#1: Protein/peptide PITUITARY ADENYLATE CYCLASE ACTIVATING POLYPEPTIDE / Pituitary adenylate cyclase-activating peptide


Mass: 2522.882 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN(RESIDUE 132-152) / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P18509

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRNOESY
221TRNOESY
NMR detailsText: Both TRNOE and NOE cross peaks were observed in the spectrum: the former reflects the conformation of PACAP21 in the receptor-bound form, while the latter reflects that of unbound PACAP21. Upon ...Text: Both TRNOE and NOE cross peaks were observed in the spectrum: the former reflects the conformation of PACAP21 in the receptor-bound form, while the latter reflects that of unbound PACAP21. Upon addition of a higher affinity ligand, PACAP27, the TRNOE cross peaks were selectively eliminated due to a competitive inhibition of the specific binding of PACAP21 to the receptor. Accordingly, the subtraction of these two spectra yields TRNOE-related cross peaks exclusively.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.7mM PACAP21; 40mM PACAP receptor; 80mM phosphate buffer (pH 6.3)90% H2O/10% D2O
21.7mM PACAP21; 40mM PACAP receptor; 80mM phosphate buffer (pH 6.3)99.8% D2O
Sample conditionsIonic strength: 0.41 / pH: 6.3 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brunger, A.T.structure solution
IRMA30-Jul-90Kaptein, R.iterative matrix relaxation
X-PLOR3.1Brunger, A.T.refinement
RefinementMethod: Iterative relaxation matrix analysis (IRMA), simulated annealing (SA)
Software ordinal: 1
Details: The structures are calculated by SA protocol of X-PLOR based on a total of 387 TRNOE-derived distance restraints obtained from the IRMA refinement.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

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