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

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Basic information

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


negative regulation of eosinophil extravasation / prostaglandin E receptor activity / Prostanoid ligand receptors / negative regulation of integrin activation / response to nematode / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / regulation of ossification / response to mechanical stimulus ...negative regulation of eosinophil extravasation / prostaglandin E receptor activity / Prostanoid ligand receptors / negative regulation of integrin activation / response to nematode / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / regulation of ossification / response to mechanical stimulus / JNK cascade / ERK1 and ERK2 cascade / positive regulation of cytokine production / bone development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / positive regulation of inflammatory response / cellular response to mechanical stimulus / cellular response to prostaglandin E stimulus / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / response to lipopolysaccharide / 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)
Similarity search - Domain/homology
Chem-8VL / Prostaglandin E2 receptor EP4 subtype
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 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
DepositionSep 28, 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 1.3Jan 16, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jan 30, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.5Nov 22, 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
A: 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)91,7184
Polymers91,2523
Non-polymers4651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-31 kcal/mol
Surface area33860 Å2
Unit cell
Length a, b, c (Å)101.970, 392.230, 81.080
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 / PGE2 receptor EP4 subtype / Prostanoid EP4 receptor


Mass: 37063.547 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 4-217, 260-366 / Mutation: 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-8VL / 4-[2-[[(2R)-2-(4-bromanylnaphthalen-1-yl)propanoyl]amino]-4-cyano-phenyl]butanoic acid


Mass: 465.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21BrN2O3

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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: 4.44 Å3/Da / Density % sol: 72.31 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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-heptanetriol, 0.2 mM ONO-AE3-208-Br, 2% DMSO
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: 0.9 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 16, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 4.2→49.339 Å / Num. obs: 22914 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 15.076 % / Biso Wilson estimate: 65.9 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.0716 / Rrim(I) all: 0.741 / Χ2: 1.446 / Net I/σ(I): 4.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.2-4.4515.3560.6760.5936370.36.99399.9
4.45-4.7615.3441.7381.5535120.711.79899.7
4.76-5.1415.3421.4942.0132350.7811.545100
5.14-5.6315.1640.9952.7330090.8471.03100
5.63-6.2914.5780.9162.7926880.8440.949100
6.29-7.2613.30.5644.424030.9270.586100
7.26-8.8814.8620.3388.5119980.9680.35100
8.88-12.5116.4480.22316.1415650.9860.23100
12.51-49.33916.0090.1918.78670.9920.19798

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WV2

5wv2
PDB Unreleased entry


Resolution: 4.2→49.339 Å / SU ML: 0.85 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.28
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.3588 1117 5.02 %
Rwork0.333 --
obs0.3343 22266 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 266.01 Å2 / Biso mean: 134.3258 Å2 / Biso min: 76.03 Å2
Refinement stepCycle: final / Resolution: 4.2→49.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5577 0 30 0 5607
Biso mean--164.4 --
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035760
X-RAY DIFFRACTIONf_angle_d0.5737852
X-RAY DIFFRACTIONf_chiral_restr0.041897
X-RAY DIFFRACTIONf_plane_restr0.005999
X-RAY DIFFRACTIONf_dihedral_angle_d13.1023432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.2001-4.39120.49551340.53782435256991
4.3912-4.62250.53891340.50452598273295
4.6225-4.91190.54841320.51242499263192
4.9119-5.29070.30361460.282327252871100
5.2907-5.82240.28021410.283627262867100
5.8224-6.66310.32141470.298527182865100
6.6631-8.38820.34611380.266227332871100
8.3882-49.34230.24161450.230527152860100

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