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- PDB-6d26: Crystal structure of the prostaglandin D2 receptor CRTH2 with fev... -

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Basic information

Entry
Database: PDB / ID: 6d26
TitleCrystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant
ComponentsProstaglandin D2 receptor 2, Endolysin chimera
KeywordsMEMBRANE PROTEIN/ANTAGONIST / GPCR / MEMBRANE PROTEIN-ANTAGONIST complex
Function / homology
Function and homology information


prostaglandin J receptor activity / prostaglandin D receptor activity / prostaglandin F receptor activity / negative regulation of male germ cell proliferation / Prostanoid ligand receptors / cellular response to prostaglandin D stimulus / positive regulation of G protein-coupled receptor signaling pathway / neuropeptide binding / neuropeptide signaling pathway / viral release from host cell by cytolysis ...prostaglandin J receptor activity / prostaglandin D receptor activity / prostaglandin F receptor activity / negative regulation of male germ cell proliferation / Prostanoid ligand receptors / cellular response to prostaglandin D stimulus / positive regulation of G protein-coupled receptor signaling pathway / neuropeptide binding / neuropeptide signaling pathway / viral release from host cell by cytolysis / peptidoglycan catabolic process / calcium-mediated signaling / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / chemotaxis / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (i) signalling events / host cell cytoplasm / neuron projection / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
Formyl peptide receptor-related / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / G-protein coupled receptors family 1 signature. / Lysozyme-like domain superfamily / G protein-coupled receptor, rhodopsin-like ...Formyl peptide receptor-related / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / G-protein coupled receptors family 1 signature. / Lysozyme-like domain superfamily / 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
fevipiprant / OLEIC ACID / TRIETHYLENE GLYCOL / S-1,2-PROPANEDIOL / SUCCINIC ACID / Endolysin / Prostaglandin D2 receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.798 Å
AuthorsWang, L. / Yao, D. / Deepak, K. / Liu, H. / Gong, W. / Fan, H. / Wei, Z. / Zhang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol. Cell / Year: 2018
Title: Structures of the Human PGD2Receptor CRTH2 Reveal Novel Mechanisms for Ligand Recognition.
Authors: Wang, L. / Yao, D. / Deepak, R.N.V.K. / Liu, H. / Xiao, Q. / Fan, H. / Gong, W. / Wei, Z. / Zhang, C.
History
DepositionApr 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 D2 receptor 2, Endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,61919
Polymers52,2291
Non-polymers2,39018
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-113 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.457, 61.710, 266.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Prostaglandin D2 receptor 2, Endolysin chimera / Chemoattractant receptor-homologous molecule expressed on Th2 cells / G-protein coupled receptor 44 ...Chemoattractant receptor-homologous molecule expressed on Th2 cells / G-protein coupled receptor 44 / Lysis protein / Lysozyme / Muramidase


Mass: 52228.727 Da / Num. of mol.: 1
Fragment: CRTH2 (UNP residues 1-236), T4 ligase (UNP residues 2-12,61-161), CRTH2 (UNP residues 238-339)
Mutation: N25A,G237ADLGLQHR,A1298C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: PTGDR2, CRTH2, DL1R, GPR44, e, T4Tp126 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y5Y4, UniProt: D9IEF7

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Non-polymers , 7 types, 21 molecules

#2: Chemical ChemComp-FSY / fevipiprant / (2-methyl-1-{[4-(methylsulfonyl)-2-(trifluoromethyl)phenyl]methyl}-1H-pyrrolo[2,3-b]pyridin-3-yl)acetic acid


Mass: 426.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17F3N2O4S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.97 Å3/Da / Density % sol: 69.03 %
Crystal growTemperature: 289 K / Method: lipidic cubic phase / pH: 6.5
Details: 100 mM MES, pH 6.5, 100 mM ammonium sulfate, 30% PEG400, 2% P400, 1 mM succinic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2017
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 19625 / % possible obs: 91.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 68.26 Å2 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.083 / Rrim(I) all: 0.202 / Χ2: 1.153 / Net I/σ(I): 5.3 / Num. measured all: 95491
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.853.90.7747820.7080.3670.8620.54276.5
2.85-2.940.7738480.7710.3790.8670.5582.6
2.9-2.964.10.7069060.8110.3360.7880.5382.7
2.96-3.024.60.6338960.8450.2860.6990.57689.9
3.02-3.084.70.60310020.8540.2670.6640.62994.8
3.08-3.154.70.5599990.8640.2520.6170.65394.4
3.15-3.2350.53110030.8960.2350.5840.67697.4
3.23-3.325.30.45110130.9020.1960.4950.75496.8
3.32-3.425.50.41210500.9250.1760.4510.86598.2
3.42-3.535.70.3519900.9250.150.3840.98796.9
3.53-3.655.40.30910640.9440.1340.3391.16698.6
3.65-3.85.40.25310460.9620.1110.2791.3998.2
3.8-3.975.20.21210180.9620.0960.2341.4296.6
3.97-4.184.70.17810230.9690.0850.1991.73794
4.18-4.444.60.1449960.9840.0690.1611.66694.5
4.44-4.784.20.1269260.9870.0620.1421.65286.2
4.78-5.264.90.129990.9880.0550.1331.72392
5.26-6.025.30.12410410.9870.0530.1361.65395.3
6.02-7.565.10.10810200.9880.0480.1191.71491.3
7.56-304.50.07710030.9910.0380.0871.57482.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C1Q

6c1q


Resolution: 2.798→29.333 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2796 973 4.98 %
Rwork0.2503 18552 -
obs0.252 19525 91.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.59 Å2 / Biso mean: 84.9894 Å2 / Biso min: 38.14 Å2
Refinement stepCycle: final / Resolution: 2.798→29.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 149 3 3642
Biso mean--94.04 55.38 -
Num. residues----447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023715
X-RAY DIFFRACTIONf_angle_d0.5945042
X-RAY DIFFRACTIONf_chiral_restr0.019568
X-RAY DIFFRACTIONf_plane_restr0.003629
X-RAY DIFFRACTIONf_dihedral_angle_d11.11331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7982-2.94560.44391120.35892181229377
2.9456-3.130.3881360.33292589272592
3.13-3.37130.34551460.30952780292696
3.3713-3.710.26961490.26822799294898
3.71-4.24550.26311430.23512783292696
4.2455-5.34360.2461400.22662653279391
5.3436-29.33480.25531470.21962767291489
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)
12.2941-0.2713-0.66711.81040.39544.3495-0.03730.5648-0.1754-0.24510.0814-0.0850.06020.1481-0.0170.4561-0.0188-0.02050.5577-0.09640.50692.014782.2726292.5409
21.73850.5316-1.67051.7285-1.32745.06650.0244-0.09640.03070.21810.14740.0996-0.2918-0.3313-0.2070.51070.0655-0.05590.4026-0.02220.572-2.217382.2904318.7889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 1241 )A5 - 1241
2X-RAY DIFFRACTION2chain 'A' and (resid 1242 through 2327 )A0

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