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- PDB-5ywy: Crystal structure of the human prostaglandin E receptor EP4 in co... -

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Basic information

Entry
Database: PDB / ID: 5ywy
TitleCrystal structure of the human prostaglandin E receptor EP4 in complex with Fab and ONO-AE3-208
Components
  • Heavy chain of Fab fragment
  • Light chain of Fab fragment
  • Prostaglandin E2 receptor EP4 subtype,Prostaglandin E2 receptor EP4 subtype
KeywordsSIGNALING PROTEIN-IMMUNE SYSTEM / G-protein coupled receptor / lipid mediator / functional antibody / SIGNALING PROTEIN-IMMUNE SYSTEM complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of eosinophil extravasation / prostaglandin E receptor activity / negative regulation of integrin activation / Prostanoid ligand receptors / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / response to mechanical stimulus / JNK cascade / response to prostaglandin E ...negative regulation of eosinophil extravasation / prostaglandin E receptor activity / negative regulation of integrin activation / Prostanoid ligand receptors / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / response to mechanical stimulus / JNK cascade / response to prostaglandin E / ERK1 and ERK2 cascade / positive regulation of cytokine production / cellular response to mechanical stimulus / bone development / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of inflammatory response / cellular response to prostaglandin E stimulus / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / immune response / inflammatory response / membrane / plasma membrane
Similarity search - Function
Prostanoid EP4 receptor / Prostaglandin DP receptor / Prostanoid receptor / 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) / Immunoglobulins / Immunoglobulin-like ...Prostanoid EP4 receptor / Prostaglandin DP receptor / Prostanoid receptor / 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) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-7UR / Prostaglandin E2 receptor EP4 subtype
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsToyoda, Y. / Morimoto, K. / Suno, R. / Horita, S. / Iwata, S. / Kobayashi, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and Technology Agency Japan
Japan Agency for Medical Research and Development Japan
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Ligand binding to human prostaglandin E receptor EP4at the lipid-bilayer interface.
Authors: Toyoda, Y. / Morimoto, K. / Suno, R. / Horita, S. / Yamashita, K. / Hirata, K. / Sekiguchi, Y. / Yasuda, S. / Shiroishi, M. / Shimizu, T. / Urushibata, Y. / Kajiwara, Y. / Inazumi, T. / ...Authors: Toyoda, Y. / Morimoto, K. / Suno, R. / Horita, S. / Yamashita, K. / Hirata, K. / Sekiguchi, Y. / Yasuda, S. / Shiroishi, M. / Shimizu, T. / Urushibata, Y. / Kajiwara, Y. / Inazumi, T. / Hotta, Y. / Asada, H. / Nakane, T. / Shiimura, Y. / Nakagita, T. / Tsuge, K. / Yoshida, S. / Kuribara, T. / Hosoya, T. / Sugimoto, Y. / Nomura, N. / Sato, M. / Hirokawa, T. / Kinoshita, M. / Murata, T. / Takayama, K. / Yamamoto, M. / Narumiya, S. / Iwata, S. / Kobayashi, T.
History
DepositionNov 30, 2017Deposition 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 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: Prostaglandin E2 receptor EP4 subtype,Prostaglandin E2 receptor EP4 subtype
H: Heavy chain of Fab fragment
L: Light chain of Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6574
Polymers91,2523
Non-polymers4041
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-30 kcal/mol
Surface area33760 Å2
Unit cell
Length a, b, c (Å)100.980, 390.150, 79.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Prostaglandin E2 receptor EP4 subtype,Prostaglandin E2 receptor EP4 subtype / PGE2 receptor EP4 subtype / Prostanoid EP4 receptor


Mass: 37063.547 Da / Num. of mol.: 1
Mutation: N7Q, A62L, G106R, N177Q, 218-259 deletion,N7Q, A62L, G106R, N177Q, 218-259 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTGER4, PTGER2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35408
#2: Antibody Heavy chain of Fab fragment / FabH


Mass: 27574.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: hybrid (others)
#3: Antibody Light chain of Fab fragment / FabL


Mass: 26614.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: hybrid (others)
#4: Chemical ChemComp-7UR / 4-[4-cyano-2-[[(2R)-2-(4-fluoranylnaphthalen-1-yl)propanoyl]amino]phenyl]butanoic acid


Mass: 404.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21FN2O3
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: 4.29 Å3/Da / Density % sol: 71.34 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 24-31% PEG 300, 150 mM potassium sulfate, 100 mM MES pH 5.5-6.5, 1% 1,2,3-heptantoriol
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 26463 / % possible obs: 99.9 % / Redundancy: 52 % / CC1/2: 0.997 / Net I/σ(I): 9
Reflection shellResolution: 3.2→3.33 Å

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Processing

Software
NameVersionClassification
PHENIXdev_2210refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.879 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.13
RfactorNum. reflection% reflection
Rfree0.2515 1324 5 %
Rwork0.2224 --
obs0.2238 26463 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 253.38 Å2 / Biso mean: 82.0147 Å2 / Biso min: 14.76 Å2
Refinement stepCycle: final / Resolution: 3.2→48.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5577 0 30 0 5607
Biso mean--117.93 --
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025760
X-RAY DIFFRACTIONf_angle_d0.6027852
X-RAY DIFFRACTIONf_chiral_restr0.041897
X-RAY DIFFRACTIONf_plane_restr0.004975
X-RAY DIFFRACTIONf_dihedral_angle_d13.2113412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.32820.34351450.301127472892100
3.3282-3.47960.32831450.272427542899100
3.4796-3.6630.30611450.252127492894100
3.663-3.89240.2751430.241827642907100
3.8924-4.19280.2211530.202827772930100
4.1928-4.61440.23091440.196327632907100
4.6144-5.28150.18171460.170228102956100
5.2815-6.65140.2021480.209528232971100
6.6514-48.8850.26971550.22722952310799
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)
12.1996-0.7797-0.69266.5165-0.26773.2806-0.035-0.03150.944-0.71160.0978-0.0957-0.83660.0189-0.08221.6579-0.5614-0.02340.6288-0.09391.6455-39.7545-24.66415.2043
20.5674-0.22070.27010.4467-0.26381.18220.086-0.131.24410.0815-0.03830.1864-0.4908-0.11290.13422.28120.21480.04550.3105-0.36621.6531-51.9652-31.12795.9079
36.8043-2.54080.37282.0005-3.45036.4076-0.06980.52581.4925-1.09330.00130.6992-1.2103-0.41610.03151.86180.42540.10480.7482-0.29041.9022-63.873-22.04619.6586
41.5431-1.41230.28682.5466-0.4660.2177-0.10730.16130.6362-0.0824-0.0760.3544-1.2541-0.0720.16452.00790.07140.12070.3683-0.13111.24-54.7367-32.3931-4.9065
53.33371.03010.4544.9413-0.07522.55050.013-0.26070.28750.19350.0474-0.0664-0.4603-0.2338-0.03360.21560.04680.07130.2233-0.0750.2011-50.578-74.49371.1334
64.14721.18580.96652.45710.10783.10120.0568-0.55970.11980.42030.17060.1458-0.0147-0.3831-0.17910.23210.10050.07440.38840.13330.1654-34.2627-101.464214.2331
71.109-0.91133.04424.8212-1.40768.9901-0.10160.2740.13280.0282-0.0402-1.0188-0.11040.86850.09310.2976-0.07570.15890.4105-0.17610.4762-27.497-77.2976-11.8225
84.334-0.43830.22056.35980.71582.952-0.1574-0.33450.54260.6050.1339-0.5422-0.65690.63670.05340.3778-0.11780.03930.2668-0.12970.3838-31.0106-69.463-6.4689
92.6813-2.12611.22582.2618-0.50280.94510.02170.09730.1534-0.0255-0.1931-0.19350.1326-0.08110.17870.1654-0.02310.03380.2363-0.05110.2141-31.6759-91.66340.0166
105.30150.96830.08966.33280.97663.2793-0.108-0.086-0.49140.20610.10720.30810.4938-0.10060.00470.1372-0.0115-0.07360.37960.03150.1552-26.1248-108.79671.9795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 49 )A18 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 122 )A50 - 122
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 156 )A123 - 156
4X-RAY DIFFRACTION4chain 'A' and (resid 157 through 346 )A157 - 346
5X-RAY DIFFRACTION5chain 'H' and (resid 20 through 138 )H20 - 138
6X-RAY DIFFRACTION6chain 'H' and (resid 139 through 242 )H139 - 242
7X-RAY DIFFRACTION7chain 'L' and (resid 23 through 40 )L23 - 40
8X-RAY DIFFRACTION8chain 'L' and (resid 41 through 112 )L41 - 112
9X-RAY DIFFRACTION9chain 'L' and (resid 113 through 150 )L113 - 150
10X-RAY DIFFRACTION10chain 'L' and (resid 151 through 236 )L151 - 236

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