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- PDB-7c4s: Sphingosine-1-phosphate receptor 3 with a natural ligand. -

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Basic information

Entry
Database: PDB / ID: 7c4s
TitleSphingosine-1-phosphate receptor 3 with a natural ligand.
Components
  • Antibody Fab fragment heavy chain
  • Antibody Fab fragment light chain
  • Sphingosine 1-phosphate receptor 3
KeywordsMEMBRANE PROTEIN / G protein-coupled receptor / Signaling protein / Agonist / natural ligand / lysophospholipid / regulator of immune system and vascular integrity.
Function / homology
Function and homology information


sphingosine-1-phosphate receptor activity / regulation of interleukin-1 beta production / negative regulation of establishment of endothelial barrier / Lysosphingolipid and LPA receptors / regulation of metabolic process / anatomical structure morphogenesis / Notch signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway ...sphingosine-1-phosphate receptor activity / regulation of interleukin-1 beta production / negative regulation of establishment of endothelial barrier / Lysosphingolipid and LPA receptors / regulation of metabolic process / anatomical structure morphogenesis / Notch signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / integrin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / Extra-nuclear estrogen signaling / inflammatory response / G protein-coupled receptor signaling pathway / lipid binding / positive regulation of cell population proliferation / plasma membrane / cytoplasm
Similarity search - Function
EDG-3 sphingosine 1-phosphate receptor / Sphingosine 1-phosphate receptor / Serpentine type 7TM GPCR chemoreceptor Srsx / 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)
Similarity search - Domain/homology
Chem-S1P / Sphingosine 1-phosphate receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
Model detailsAgonist bound GPCR stabilized by specific antibody Fab fragment
AuthorsIwata, S. / Maeda, S. / Luo, F. / Nango, E. / hirata, K. / Asada, H.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)P19am0101070 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101079 Japan
Japan Society for the Promotion of Science (JSPS)19J22636 Japan
Japan Society for the Promotion of Science (JSPS)18H02394 Japan
Japan Society for the Promotion of Science (JSPS)19H05776 Japan
Japan Society for the Promotion of Science (JSPS)19H05777 Japan
Japan Society for the Promotion of Science (JSPS)15H05721 Japan
CitationJournal: Sci Adv / Year: 2021
Title: Endogenous agonist-bound S1PR3 structure reveals determinants of G protein-subtype bias.
Authors: Maeda, S. / Shiimura, Y. / Asada, H. / Hirata, K. / Luo, F. / Nango, E. / Tanaka, N. / Toyomoto, M. / Inoue, A. / Aoki, J. / Iwata, S. / Hagiwara, M.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Antibody Fab fragment light chain
H: Antibody Fab fragment heavy chain
A: Sphingosine 1-phosphate receptor 3
K: Antibody Fab fragment light chain
J: Antibody Fab fragment heavy chain
B: Sphingosine 1-phosphate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,3608
Polymers178,6016
Non-polymers7592
Water0
1
L: Antibody Fab fragment light chain
H: Antibody Fab fragment heavy chain
A: Sphingosine 1-phosphate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6804
Polymers89,3013
Non-polymers3791
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-38 kcal/mol
Surface area34440 Å2
MethodPISA
2
K: Antibody Fab fragment light chain
J: Antibody Fab fragment heavy chain
B: Sphingosine 1-phosphate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6804
Polymers89,3013
Non-polymers3791
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-39 kcal/mol
Surface area34420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.480, 247.080, 98.610
Angle α, β, γ (deg.)90.000, 97.370, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 14 through 64 or resid 75...
21(chain B and (resid 14 through 64 or resid 75...
12chain H
22chain J
13chain K
23chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 14 through 64 or resid 75...A14 - 64
121(chain A and (resid 14 through 64 or resid 75...A75 - 101
131(chain A and (resid 14 through 64 or resid 75...A103 - 136
141(chain A and (resid 14 through 64 or resid 75...A140 - 141
151(chain A and (resid 14 through 64 or resid 75...A144 - 149
161(chain A and (resid 14 through 64 or resid 75...A152 - 222
171(chain A and (resid 14 through 64 or resid 75...A224 - 2240
181(chain A and (resid 14 through 64 or resid 75...A242 - 306
191(chain A and (resid 14 through 64 or resid 75...A308306
1101(chain A and (resid 14 through 64 or resid 75...A308
211(chain B and (resid 14 through 64 or resid 75...B14 - 64
221(chain B and (resid 14 through 64 or resid 75...B75 - 101
231(chain B and (resid 14 through 64 or resid 75...B103 - 136
241(chain B and (resid 14 through 64 or resid 75...B140 - 141
251(chain B and (resid 14 through 64 or resid 75...B14 - 311
261(chain B and (resid 14 through 64 or resid 75...B152 - 222
271(chain B and (resid 14 through 64 or resid 75...B224 - 240
281(chain B and (resid 14 through 64 or resid 75...B242 - 306
291(chain B and (resid 14 through 64 or resid 75...B308
112chain HH1 - 219
212chain JJ1 - 219
113chain KK1 - 214
213chain LL1 - 214

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Antibody Fab fragment light chain


Mass: 23649.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Culture medium of monoclonal hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: MRL/lpr
#2: Antibody Antibody Fab fragment heavy chain


Mass: 23338.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Culture medium of monoclonal hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: MRL/lpr
#3: Protein Sphingosine 1-phosphate receptor 3 / 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


Mass: 42313.336 Da / Num. of mol.: 2 / Mutation: N15Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Sf9 / Gene: S1PR3, EDG3 / Plasmid: pF9A / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99500
#4: Chemical ChemComp-S1P / (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate / sphingosine 1-phosphate / Sphingosine-1-phosphate


Mass: 379.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38NO5P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 100 mM Tris-HCl, 36% PEG 400, 80 mM Lithium Citrate
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→43.48 Å / Num. obs: 30984 / % possible obs: 100 % / Redundancy: 59.872 % / Biso Wilson estimate: 101.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.732 / Rrim(I) all: 0.738 / Χ2: 0.649 / Net I/σ(I): 11.02 / Num. measured all: 1855076 / Scaling rejects: 399
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible allRmerge(I) obs
3.2-3.3953.4681.2849340.66312.686100
3.39-3.6257.2432.6546160.8613.7871003.754
3.62-3.963.5634.2343140.9312.22999.92.212
3.9-4.2663.2547.2439760.9731.2871.277
4.26-4.7562.68812.2136400.990.7350.729
4.75-5.4561.20116.1132030.9950.5199.90.506
5.45-6.656.13616.6327520.9950.4440.44
6.6-9.0361.52428.6621520.9990.22499.90.222
9.03-43.4864.58651.8313970.9980.13599.10.134

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V2Y, 5XLI

3v2y

5xli


Resolution: 3.2→43.48 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 1520 4.91 %
Rwork0.2419 29433 -
obs0.2429 30953 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182 Å2 / Biso mean: 81.6066 Å2 / Biso min: 48.26 Å2
Refinement stepCycle: final / Resolution: 3.2→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11060 0 50 0 11110
Biso mean--79.44 --
Num. residues----1428
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2242X-RAY DIFFRACTION8.211TORSIONAL
12B2242X-RAY DIFFRACTION8.211TORSIONAL
21H2005X-RAY DIFFRACTION8.211TORSIONAL
22J2005X-RAY DIFFRACTION8.211TORSIONAL
31K2060X-RAY DIFFRACTION8.211TORSIONAL
32L2060X-RAY DIFFRACTION8.211TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.30.36081370.379126602797100
3.3-3.420.34541370.305826682805100
3.42-3.560.28131380.295126622800100
3.56-3.720.28851390.274726912830100
3.72-3.920.30281390.264926552794100
3.92-4.160.28611290.237926802809100
4.16-4.480.24851330.220127022835100
4.48-4.930.231540.213526542808100
4.93-5.640.23821440.219426732817100
5.65-7.110.30251350.250526852820100
7.11-43.480.21021350.2082703283899

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