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- PDB-2d2p: The solution structure of micelle-bound peptide -

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Basic information

Entry
Database: PDB / ID: 2d2p
TitleThe solution structure of micelle-bound peptide
ComponentsPituitary adenylate cyclase activating polypeptide-38
KeywordsHORMONE/GROWTH FACTOR / HORMONE-GROWTH FACTOR COMPLEX
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 / regulation of G protein-coupled receptor signaling pathway / neuropeptide hormone activity / insulin secretion / peptide hormone receptor binding / negative regulation of cell cycle / neuropeptide signaling pathway ...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 / regulation of G protein-coupled receptor signaling pathway / neuropeptide hormone activity / insulin secretion / peptide hormone receptor binding / negative regulation of cell cycle / neuropeptide signaling pathway / positive regulation of protein kinase activity / activation of adenylate cyclase activity / cAMP-mediated signaling / positive regulation of GTPase activity / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / neuron projection development / cell-cell signaling / positive regulation of cold-induced thermogenesis / regulation of protein localization / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / perikaryon / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, MOLECULAR DYNAMICS, ENERGY MINIMIZATION
AuthorsTateishi, Y. / Jee, J.G. / Inooka, H. / Tochio, H. / Hiroaki, H. / Shirakawa, M.
CitationJournal: To be Published
Title: The solution structure of micelle-bound peptide
Authors: Tateishi, Y. / Jee, J.G. / Inooka, H. / Tochio, H. / Hiroaki, H. / Shirakawa, M.
History
DepositionSep 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pituitary adenylate cyclase activating polypeptide-38


Theoretical massNumber of molelcules
Total (without water)4,5451
Polymers4,5451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Pituitary adenylate cyclase activating polypeptide-38 / PACAP-38 / PACAP38


Mass: 4545.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18509
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.5mM PACAP38 U-15N,13C; 20mM potassium phosphate buffer; 200mM DPC; 93% H2O, 5% D2O, 2% Glycerol-1,1,2,3,3-d5
Solvent system: 93% H2O, 5% D2O, 2% Glycerol-1,1,2,3,3-d5
Sample conditionsIonic strength: 20mM potassium phosphate / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2.1DELAGLIOprocessing
Sparky3.11Goddarddata analysis
CYANA2.0.17GUENTERTstructure solution
Amber8refinement
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, MOLECULAR DYNAMICS, ENERGY MINIMIZATION
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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