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- PDB-2ksa: Substance P in DMPC/CHAPS isotropic q=0.25 bicelles as a ligand f... -

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Basic information

Entry
Database: PDB / ID: 2ksa
TitleSubstance P in DMPC/CHAPS isotropic q=0.25 bicelles as a ligand for NK1R
Components
  • Substance P
  • Substance-P receptor
KeywordsNEUROPEPTIDE RECEPTOR/NEUROPEPTIDE / Substance P / DMPC/CHAPS bicelle / Autodock / NK1R / NEUROPEPTIDE RECEPTOR-NEUROPEPTIDE complex
Function / homology
Function and homology information


substance P receptor binding / substance P receptor activity / tachykinin receptor activity / positive regulation of flagellated sperm motility / insemination / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of uterine smooth muscle contraction / positive regulation of synaptic transmission, cholinergic / detection of abiotic stimulus ...substance P receptor binding / substance P receptor activity / tachykinin receptor activity / positive regulation of flagellated sperm motility / insemination / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of uterine smooth muscle contraction / positive regulation of synaptic transmission, cholinergic / detection of abiotic stimulus / tachykinin receptor signaling pathway / operant conditioning / positive regulation of lymphocyte proliferation / sperm head / response to ozone / sperm ejaculation / positive regulation of action potential / response to auditory stimulus / regulation of smooth muscle cell proliferation / smooth muscle contraction involved in micturition / positive regulation of blood pressure / positive regulation of hormone secretion / positive regulation of vascular permeability / regulation of smooth muscle cell migration / positive regulation of ossification / positive regulation of leukocyte migration / eating behavior / response to pain / positive regulation of epithelial cell migration / behavioral response to pain / associative learning / angiotensin-mediated drinking behavior / neuropeptide signaling pathway / sperm flagellum / response to electrical stimulus / long-term memory / positive regulation of vasoconstriction / positive regulation of stress fiber assembly / sperm midpiece / sensory perception of pain / positive regulation of epithelial cell proliferation / cellular response to nerve growth factor stimulus / response to progesterone / positive regulation of synaptic transmission, GABAergic / response to nicotine / Cargo recognition for clathrin-mediated endocytosis / cell-cell signaling / response to estradiol / Clathrin-mediated endocytosis / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / cell body / chemical synaptic transmission / G alpha (q) signalling events / response to ethanol / inflammatory response / axon / neuronal cell body / dendrite / synapse / cell surface / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Tachykinin family / Tachykinin family / Tachykinin domain / Tachykinin family / Neurokinin NK1 receptor / Neurokinin receptor / Tachykinin/Neurokinin-like, conserved site / Tachykinin family signature. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins ...Tachykinin family / Tachykinin family / Tachykinin domain / Tachykinin family / Neurokinin NK1 receptor / Neurokinin receptor / Tachykinin/Neurokinin-like, conserved site / Tachykinin family signature. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protachykinin-1 / Substance-P receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailsrandomly chosen, model 1
AuthorsGayen, A. / Mukhopadhyay, C.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: NMR evidence of GM1-induced conformational change of Substance P using isotropic bicelles
Authors: Gayen, A. / Goswami, S.K. / Mukhopadhyay, C.
History
DepositionDec 31, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Substance-P receptor
B: Substance P


Theoretical massNumber of molelcules
Total (without water)43,0302
Polymers43,0302
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)5 / 20highest binding energy
RepresentativeModel #1randomly chosen

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Components

#1: Protein Substance-P receptor / SPR / NK-1 receptor / NK-1R / Tachykinin receptor 1


Mass: 41679.840 Da / Num. of mol.: 1 / Fragment: UNP residues 1-364 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25103
#2: Protein/peptide Substance P


Mass: 1350.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P20366

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: this is a 5 conformation ensemble structure of SP-NK1 complex modeled running Autodock using experimental solution conformation of SP in DMPC/CHAPS bicelles from XPLOR-NIH
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY

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Sample preparation

DetailsContents: 3.7 mM Substance P-1, 18.5 mM DMPC-2, 74.0 mM CHAPS-3, unapplicable mM H2O-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentSolution-ID
3.7 mMSubstance P-11
18.5 mMDMPC-21
74.0 mMCHAPS-31
mMH2O-41
Sample conditionsIonic strength: minimum / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
SPARKY-win32Thomas Goddardprocessing
XPLOR-NIH2.17.0Charles Schwietersstructure solution
AutoDock4Arthur J. Olsonstructure solution
XPLOR-NIH2.17.0Charles Schwietersgeometry optimization
AutoDock4Arthur J. Olsongeometry optimization
AutoDock4Arthur J. Olsonrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: substance P with NK1, substance P in DMPC/CHAPS bicelles from XPLOR; The structures are produced after docking using AUTODOCK using experimental NMR on Chain B
NMR representativeSelection criteria: randomly chosen
NMR ensembleConformer selection criteria: highest binding energy / Conformers calculated total number: 20 / Conformers submitted total number: 5 / Representative conformer: 1

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