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- PDB-6m9t: Crystal structure of EP3 receptor bound to misoprostol-FA -

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Basic information

Entry
Database: PDB / ID: 6m9t
TitleCrystal structure of EP3 receptor bound to misoprostol-FA
ComponentsProstaglandin E2 receptor EP3 subtype, Endolysin chimera
KeywordsMEMBRANE PROTEIN / GPCR / prostaglandin E2 receptor 3 (EP3) / prostaglandin analogue / misoprostol-FA (biologically active free acid) / XFEL / LCP / T4L
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 / viral release from host cell by cytolysis / peptidoglycan catabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process ...negative regulation of gastric acid secretion / intestine smooth muscle contraction / prostaglandin E receptor activity / Prostanoid ligand receptors / cell death / positive regulation of fever generation / viral release from host cell by cytolysis / peptidoglycan catabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / nuclear envelope / phospholipase C-activating G protein-coupled receptor signaling pathway / lysozyme activity / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / host cell cytoplasm / defense response to bacterium / inflammatory response / G protein-coupled receptor signaling pathway / membrane / plasma membrane
Similarity search - Function
Prostanoid EP3 receptor / Prostanoid EP3 receptor, type 2 / Prostaglandin DP receptor / Prostanoid receptor / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G protein-coupled receptor, rhodopsin-like ...Prostanoid EP3 receptor / Prostanoid EP3 receptor, type 2 / Prostaglandin DP receptor / Prostanoid receptor / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-J9P / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Endolysin / Prostaglandin E2 receptor EP3 subtype
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAudet, M. / White, K.L. / Breton, B. / Zarzycka, B. / Han, G.W. / Lu, Y. / Gati, C. / Batyuk, A. / Popov, P. / Velasquez, J. ...Audet, M. / White, K.L. / Breton, B. / Zarzycka, B. / Han, G.W. / Lu, Y. / Gati, C. / Batyuk, A. / Popov, P. / Velasquez, J. / Manahan, D. / Hu, H. / Weierstall, U. / Liu, W. / Shui, W. / Katrich, V. / Cherezov, V. / Hanson, M.A. / Stevens, R.C.
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Crystal structure of misoprostol bound to the labor inducer prostaglandin E2receptor.
Authors: Audet, M. / White, K.L. / Breton, B. / Zarzycka, B. / Han, G.W. / Lu, Y. / Gati, C. / Batyuk, A. / Popov, P. / Velasquez, J. / Manahan, D. / Hu, H. / Weierstall, U. / Liu, W. / Shui, W. / ...Authors: Audet, M. / White, K.L. / Breton, B. / Zarzycka, B. / Han, G.W. / Lu, Y. / Gati, C. / Batyuk, A. / Popov, P. / Velasquez, J. / Manahan, D. / Hu, H. / Weierstall, U. / Liu, W. / Shui, W. / Katritch, V. / Cherezov, V. / Hanson, M.A. / Stevens, R.C.
History
DepositionAug 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 29, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 11, 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 EP3 subtype, Endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,26311
Polymers60,0231
Non-polymers2,23910
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-50 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.800, 54.850, 96.800
Angle α, β, γ (deg.)90.00, 95.83, 90.00
Int Tables number5
Space group name H-MC121
DetailsAuthors state that the biological unit is unknown.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Prostaglandin E2 receptor EP3 subtype, Endolysin chimera / PGE2 receptor EP3 subtype / PGE2-R / Prostanoid EP3 receptor / Lysis protein / Lysozyme / Muramidase


Mass: 60023.445 Da / Num. of mol.: 1
Fragment: EP3 UNP residues 2-259,273-353 with intervening lysozyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: PTGER3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43115, UniProt: P00720, lysozyme

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Non-polymers , 5 types, 15 molecules

#2: Chemical ChemComp-J9P / (11alpha,12alpha,13E,16S)-11,16-dihydroxy-16-methyl-9-oxoprost-13-en-1-oic acid


Mass: 368.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36O5
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM sodium citrate, pH 3.8-4.2, 10-35 mM magnesium sulfate, 20-23% v/v PEG400, 2.5% Jeffamine M-600

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.302 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Aug 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.302 Å / Relative weight: 1
ReflectionResolution: 2.5→30.03 Å / Num. obs: 22151 / % possible obs: 100 % / Redundancy: 223.9 % / Biso Wilson estimate: 74.95 Å2 / CC1/2: 0.9944 / R split: 0.01 / Net I/σ(I): 4.2
Reflection shellResolution: 2.5→2.62 Å / Redundancy: 90.5 % / Mean I/σ(I) obs: 0.25 / Num. unique obs: 22097 / CC1/2: 0.193 / R split: 4.791 / % possible all: 100
Serial crystallography measurementCollection time total: 1.75 hours / Collimation: KB mirrors / Pulse duration: 40 fsec. / Pulse photon energy: 9.52 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Flow rate: 0.22 µL/min / Injector diameter: 50 µm / Injector nozzle: LCP / Power by: HPLC pump
Serial crystallography data reductionCrystal hits: 32143 / Frames failed index: 3643 / Frames indexed: 28500 / Frames total: 1311952 / Lattices indexed: 28500 / XFEL run numbers: 146-156

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3P0G & 4EIY

3p0g

4eiy


Resolution: 2.5→27.27 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.315 / SU Rfree Blow DPI: 0.234 / SU Rfree Cruickshank DPI: 0.242
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1050 4.75 %RANDOM
Rwork0.2 ---
obs0.202 22101 100 %-
Displacement parametersBiso mean: 128.85 Å2
Baniso -1Baniso -2Baniso -3
1--5.0572 Å20 Å220.0275 Å2
2---3.0975 Å20 Å2
3---8.1547 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: 1 / Resolution: 2.5→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 127 5 3548
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093630HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.954909HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1257SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes530HARMONIC5
X-RAY DIFFRACTIONt_it3630HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.88
X-RAY DIFFRACTIONt_other_torsion18.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion479SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3985SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.341 127 4.34 %
Rwork0.279 2798 -
all0.282 2925 -
obs--99.97 %
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)
12.95040.04811.1552.56180.84264.3817-0.159-0.23160.16670.05430.10920.3195-0.1149-0.57220.0498-1.04750.0099-0.0409-0.80360.0578-1.1661126.1788-10.9319145.6804
26.1972-0.21255.09484.1803-0.485912.5595-0.15280.32830.3114-0.4009-0.1887-0.2772-0.6020.98010.3415-0.7657-0.1645-0.2056-0.62510.0782-1.3404119.9708-17.1007102.9829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|46 - A|259 A|273 - A|353 }
2X-RAY DIFFRACTION2{ A|1000 - A|1163 }

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