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- PDB-6ak3: Crystal structure of the human prostaglandin E receptor EP3 bound... -

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Basic information

Entry
Database: PDB / ID: 6ak3
TitleCrystal structure of the human prostaglandin E receptor EP3 bound to prostaglandin E2
ComponentsProstaglandin E2 receptor EP3 subtype,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / GPCR / lipid / signaling protein / prostanoid receptor
Function / homology
Function and homology information


negative regulation of gastric acid secretion / intestine smooth muscle contraction / prostaglandin E receptor activity / Prostanoid ligand receptors / cell death / positive regulation of fever generation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / nuclear envelope / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events ...negative regulation of gastric acid secretion / intestine smooth muscle contraction / prostaglandin E receptor activity / Prostanoid ligand receptors / cell death / positive regulation of fever generation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / nuclear envelope / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / electron transfer activity / periplasmic space / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / membrane / plasma membrane
Similarity search - Function
Prostanoid EP3 receptor / Prostanoid EP3 receptor, type 2 / Prostaglandin DP receptor / Prostanoid receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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-P2E / Chem-POV / Soluble cytochrome b562 / Prostaglandin E2 receptor EP3 subtype
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsMorimoto, K. / Suno, R. / Iwata, S. / Kobayashi, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18gm0910007 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101079 Japan
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Crystal structure of the endogenous agonist-bound prostanoid receptor EP3.
Authors: Morimoto, K. / Suno, R. / Hotta, Y. / Yamashita, K. / Hirata, K. / Yamamoto, M. / Narumiya, S. / Iwata, S. / Kobayashi, T.
History
DepositionAug 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
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
B: Prostaglandin E2 receptor EP3 subtype,Soluble cytochrome b562
A: Prostaglandin E2 receptor EP3 subtype,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3146
Polymers92,0892
Non-polymers2,2254
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-12 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.090, 42.280, 161.300
Angle α, β, γ (deg.)90.00, 96.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Prostaglandin E2 receptor EP3 subtype,Soluble cytochrome b562 / PGE2 receptor EP3 subtype / PGE2-R / Prostanoid EP3 receptor / Cytochrome b-562


Mass: 46044.707 Da / Num. of mol.: 2
Mutation: A173I,V185S,N217Q,S258D,C289L,N308Q,M1007W,R1098I,H1102I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: PTGER3, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43115, UniProt: P0ABE7
#2: Chemical ChemComp-P2E / (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid / Prostaglandin E2 / Prostaglandin E2


Mass: 352.465 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32O5 / Comment: medication*YM
#3: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM

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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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: buffer A (0.1 M MES-NaOH (pH 6.0), 35 % PEG300, 400 mM Na2SO4, 1% 1,2,3-heptanetriol, 0.2 mM ONO-AE3-240), buffer B (0.1 M MES-NaOH (pH 5.5-6.0), 30-40 % PEG300, 100 mM NaCl, 100 mM Li2SO4, ...Details: buffer A (0.1 M MES-NaOH (pH 6.0), 35 % PEG300, 400 mM Na2SO4, 1% 1,2,3-heptanetriol, 0.2 mM ONO-AE3-240), buffer B (0.1 M MES-NaOH (pH 5.5-6.0), 30-40 % PEG300, 100 mM NaCl, 100 mM Li2SO4, 1% 1,2,3-heptanetriol, 0.2 mM ONO-AE3-240), buffer C (0.1 M MES-NaOH (pH 6.1) or 0.1 M Tris-HCl (pH 7.5-8.0), 30 % PEG500MME, 200 mM (NH4)2SO4, 1% 1,2,3-heptanetriol, 0.2 mM ONO-AE3-240), buffer D (0.1 M MES-NaOH (pH 5.8-6.1), 30 % PEG300, 100 mM MgSO4, 1% 1,2,3-heptanetriol, 0.2 mM ONO-AE3-240), buffer E (0.1 M MES-NaOH (pH 5.5), 30 % PEG300, 100 mM K2SO4, 1% 1,2,3-heptanetriol, 0.2 mM ONO-AE3-240)

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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: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 20206 / % possible obs: 99.9 % / Redundancy: 43.4 % / Net I/σ(I): 1.15
Reflection shellResolution: 2.9→3.08 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.9→48.377 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2952 967 4.79 %
Rwork0.2508 --
obs0.2529 20175 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→48.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4109 0 142 0 4251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024329
X-RAY DIFFRACTIONf_angle_d0.4375830
X-RAY DIFFRACTIONf_dihedral_angle_d11.9242480
X-RAY DIFFRACTIONf_chiral_restr0.035702
X-RAY DIFFRACTIONf_plane_restr0.003679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.0530.34861290.29412695X-RAY DIFFRACTION100
3.053-3.24420.30041510.26722718X-RAY DIFFRACTION100
3.2442-3.49470.29451200.23612726X-RAY DIFFRACTION100
3.4947-3.84620.25221420.222730X-RAY DIFFRACTION100
3.8462-4.40240.29711450.22472712X-RAY DIFFRACTION100
4.4024-5.54530.29071310.25182782X-RAY DIFFRACTION100
5.5453-48.38390.30631490.27932845X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.07651.47630.20123.14330.74653.2029-0.068-0.00030.1724-0.0221-0.04630.1104-0.39980.093-0.07130.138-0.0708-0.0010.11050.05970.431665.896455.2678211.8119
23.94450.73460.49842.70740.39461.8476-0.05480.24030.7531-0.28560.05590.5763-0.3771-0.1006-0.14230.16110.0005-0.01760.22260.13610.729451.173753.8619210.6267
33.79851.17760.32151.92320.05642.24760.03230.2765-0.0673-0.04240.20050.06560.3411-0.2258-0.20330.0011-0.0946-0.11890.19430.13570.34954.773939.6636209.2063
41.0013-0.56490.25951.2816-0.8781.7124-0.02580.57-0.438-0.47330.02560.44110.3363-0.2688-0.31130.299-0.2382-0.11040.5917-0.1950.425667.539238.8477190.9427
53.41721.16920.05562.7431-0.20363.3262-0.05190.1905-0.3683-0.27940.1494-0.15970.2958-0.0641-0.13790.1886-0.112-0.02490.1528-0.15130.397380.635234.743208.8639
63.44050.87930.09342.6756-0.21991.58440.17710.0874-0.6133-0.26230.2032-0.37480.28920.1973-0.06820.13680.0346-0.02280.2155-0.12210.662295.074734.18210.3399
73.29320.73750.36261.95420.15270.9691-0.06810.1161-0.0773-0.20640.0588-0.2869-0.00460.2369-0.027-0.0012-0.1318-0.01190.3001-0.06570.352896.580747.0508210.717
83.31071.1747-0.21492.744-0.07690.50660.09860.09520.1842-0.05750.0370.0751-0.14550.0465-0.04150.0683-0.04490.05090.1225-0.01670.284988.185348.9576210.4439
91.1242-0.5864-0.7280.59670.95681.6152-0.1010.77750.5754-0.44790.0154-0.4068-0.35750.2051-0.14250.2974-0.17040.03580.57940.26880.36881.04652.2088188.5217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 47 through 124 )
2X-RAY DIFFRACTION2chain 'B' and (resid 125 through 226 )
3X-RAY DIFFRACTION3chain 'B' and (resid 227 through 346 )
4X-RAY DIFFRACTION4chain 'B' and (resid 347 through 1106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 47 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 202 )
7X-RAY DIFFRACTION7chain 'A' and (resid 203 through 263 )
8X-RAY DIFFRACTION8chain 'A' and (resid 264 through 346 )
9X-RAY DIFFRACTION9chain 'A' and (resid 347 through 1106 )

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