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- PDB-9w0l: S1P3 in complex with CYM52581 and spm242 -

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Basic information

Entry
Database: PDB / ID: 9w0l
TitleS1P3 in complex with CYM52581 and spm242
ComponentsSphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase
KeywordsMEMBRANE PROTEIN / S1P3
Function / homology
Function and homology information


negative regulation of establishment of endothelial barrier / sphingosine-1-phosphate receptor activity / Lysosphingolipid and LPA receptors / regulation of interleukin-1 beta production / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / anatomical structure morphogenesis / Notch signaling pathway / integrin binding ...negative regulation of establishment of endothelial barrier / sphingosine-1-phosphate receptor activity / Lysosphingolipid and LPA receptors / regulation of interleukin-1 beta production / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / anatomical structure morphogenesis / Notch signaling pathway / integrin binding / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynapse / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / inflammatory response / positive regulation of cell population proliferation / lipid binding / plasma membrane / cytoplasm
Similarity search - Function
EDG-3 sphingosine 1-phosphate receptor / Sphingosine 1-phosphate receptor / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. ...EDG-3 sphingosine 1-phosphate receptor / Sphingosine 1-phosphate receptor / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / Concanavalin A-like lectin/glucanase domain superfamily / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / : / Endo-1,4-beta-xylanase / Sphingosine 1-phosphate receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Niallia circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsBeili, W. / Qiang, Z. / Qiuxiang, T.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Protein Cell / Year: 2025
Title: Structural basis of allosteric and bitopic ligands binding in sphingosine-1-phosphate receptors 2 and 3.
Authors: Yanhong Wu / Qiuru Chen / Hongyu Wang / Kezhen Liu / Jiaxin Wei / Mu Wang / Kun Chen / Ya Zhu / Shuo Han / Cuiying Yi / Limin Ma / Gisela Schnapp / Alexander Pautsch / Christian Gnamm / ...Authors: Yanhong Wu / Qiuru Chen / Hongyu Wang / Kezhen Liu / Jiaxin Wei / Mu Wang / Kun Chen / Ya Zhu / Shuo Han / Cuiying Yi / Limin Ma / Gisela Schnapp / Alexander Pautsch / Christian Gnamm / Matthias Grauert / Esther Schmidt / Qiuxiang Tan / Beili Wu / Qiang Zhao /
History
DepositionJul 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2693
Polymers54,3561
Non-polymers9132
Water00
1
A: Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase
hetero molecules

A: Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5376
Polymers108,7112
Non-polymers1,8264
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area3140 Å2
ΔGint-20 kcal/mol
Surface area40100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.570, 299.580, 67.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase / S1P receptor 3 / S1P3 / Endothelial differentiation G-protein coupled receptor 3 / Sphingosine 1- ...S1P receptor 3 / S1P3 / Endothelial differentiation G-protein coupled receptor 3 / Sphingosine 1-phosphate receptor Edg-3 / S1P receptor Edg-3 / Xylanase / 1 / 4-beta-D-xylan xylanohydrolase


Mass: 54355.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Niallia circulans (bacteria)
Gene: S1PR3, C9orf108, C9orf47, EDG3, xlnA / Production host: Puma concolor (puma)
References: UniProt: Q99500, UniProt: P09850, endo-1,4-beta-xylanase
#2: Chemical ChemComp-A1EUC / [(2~{R})-2-azanyl-4-[2-chloranyl-4-(3-hydroxyphenyl)sulfanyl-phenyl]-2-(hydroxymethyl)butyl] dihydrogen phosphate


Mass: 433.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21ClNO6PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1EUD / ~{N}-[(~{R})-(5-bromanylpyridin-2-yl)-(3,4-dichlorophenyl)methyl]-4-cyano-3-fluoranyl-benzamide


Mass: 479.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H11BrCl2FN3O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.47 Å3/Da / Density % sol: 64.59 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 100 mM Tris-HCl, pH 8.0, 20% PEG600, 60 mM Li2SO4, 15% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→29.7 Å / Num. obs: 9019 / % possible obs: 99.53 % / Redundancy: 7.3 % / Rpim(I) all: 0.05 / Net I/σ(I): 4.4
Reflection shellResolution: 3.6→3.7 Å / Num. unique obs: 886 / Rpim(I) all: 0.02

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→29.66 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.281 451 5 %
Rwork0.2314 --
obs0.2338 9019 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 55 0 3748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013853
X-RAY DIFFRACTIONf_angle_d1.1825271
X-RAY DIFFRACTIONf_dihedral_angle_d5.555559
X-RAY DIFFRACTIONf_chiral_restr0.078599
X-RAY DIFFRACTIONf_plane_restr0.008681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-4.120.36361470.26522797X-RAY DIFFRACTION100
4.12-5.190.26621480.21292825X-RAY DIFFRACTION100
5.19-5.80.2421560.22552946X-RAY DIFFRACTION100

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