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- PDB-2dco: S1P4 First Extracellular Loop Peptidomimetic -

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Basic information

Entry
Database: PDB / ID: 2dco
TitleS1P4 First Extracellular Loop Peptidomimetic
ComponentsS1P4 First Extracellular Loop Peptidomimetic
KeywordsMEMBRANE PROTEIN / coiled coil / disulfide / helix-turn-helix / 3-10 helix
Function / homology
Function and homology information


membrane curvature sensor activity / sphingosine-1-phosphate receptor activity / Lysosphingolipid and LPA receptors / Retrograde transport at the Trans-Golgi-Network / regulation of Arp2/3 complex-mediated actin nucleation / GTP-dependent protein binding / protein localization to phagophore assembly site / regulation of metabolic process / ruffle organization / phosphatidylinositol-4-phosphate binding ...membrane curvature sensor activity / sphingosine-1-phosphate receptor activity / Lysosphingolipid and LPA receptors / Retrograde transport at the Trans-Golgi-Network / regulation of Arp2/3 complex-mediated actin nucleation / GTP-dependent protein binding / protein localization to phagophore assembly site / regulation of metabolic process / ruffle organization / phosphatidylinositol-4-phosphate binding / lamellipodium assembly / small GTPase-mediated signal transduction / plasma membrane => GO:0005886 / mitophagy / : / ruffle / trans-Golgi network membrane / G protein-coupled receptor activity / intracellular protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / phospholipid binding / small GTPase binding / cell cortex / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / actin cytoskeleton organization / cadherin binding / immune response / G protein-coupled receptor signaling pathway / protein domain specific binding / lipid binding / nucleolus / GTP binding / Golgi apparatus / mitochondrion / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
EDG-6 sphingosine 1-phosphate receptor / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / Sphingosine 1-phosphate receptor / AH/BAR domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...EDG-6 sphingosine 1-phosphate receptor / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / Sphingosine 1-phosphate receptor / AH/BAR domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Sphingosine 1-phosphate receptor 4 / Arfaptin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, matrix relaxation, torsion angle dynamics, energy minimization
AuthorsPham, T.C.T. / Kriwacki, R.W. / Parrill, A.L.
CitationJournal: Biopolymers / Year: 2007
Title: Peptide design and structural characterization of a GPCR loop mimetic
Authors: Pham, T.C.T. / Kriwacki, R.W. / Parrill, A.L.
History
DepositionJan 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S1P4 First Extracellular Loop Peptidomimetic


Theoretical massNumber of molelcules
Total (without water)3,8911
Polymers3,8911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1extended first helix

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Components

#1: Protein/peptide S1P4 First Extracellular Loop Peptidomimetic / Arfaptin-2 / ADP-ribosylation factor-interacting protein 2 / Partner of RAC1 / Protein ...Arfaptin-2 / ADP-ribosylation factor-interacting protein 2 / Partner of RAC1 / Protein POR1phingosine 1-phosphate receptor Edg-6 / S1P receptor Edg-6 / Endothelial differentiation G-protein coupled receptor 6 / Sphingosine 1-phosphate receptor 4 / S1P4


Mass: 3891.223 Da / Num. of mol.: 1 / Fragment: Extracellular Loop 1 / Mutation: L10C/A28C
Source method: isolated from a genetically manipulated source
Details: This protein is a fusion protein. Residues 13-26 and 29-30 are from the first extracellular loop of S1P4 receptor. The rest, residues 3-12, 27-28, and 31-34 are from Arfatin (PDB entry 1I49) ...Details: This protein is a fusion protein. Residues 13-26 and 29-30 are from the first extracellular loop of S1P4 receptor. The rest, residues 3-12, 27-28, and 31-34 are from Arfatin (PDB entry 1I49) segments 139-148, 164-164, 168-171 of 1I49 that we designed to be in the sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: S1P4 / Plasmid: pET-32a, CCE1a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53365, UniProt: O95977

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2123D 15N-separated NOESY
2223D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM CCE1a U-15N; 10mM phosphate buffer pH 6; 20% TFE-d3, 0.025% NaN320% TFE-d3
23mM CCE1a U-15N,13C; 10mM phosphate buffer pH 6; 20% TFE-d3, 0.025% NaN320% TFE-d3
Sample conditionsIonic strength: 0.06 mol/kg / pH: 6.0 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3.1Delaglioprocessing
Felix98Accelerysdata analysis
CNS1.1Brungerstructure solution
ARIA1.2Lingerefinement
Amber8Caserefinement
RefinementMethod: simulated annealing, matrix relaxation, torsion angle dynamics, energy minimization
Software ordinal: 1
Details: the structures are based on a total of 748 NOE-derived distance constraints
NMR representativeSelection criteria: extended first helix
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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