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- PDB-7m8w: XFEL crystal structure of the prostaglandin D2 receptor CRTH2 in ... -

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Basic information

Entry
Database: PDB / ID: 7m8w
TitleXFEL crystal structure of the prostaglandin D2 receptor CRTH2 in complex with 15R-methyl-PGD2
ComponentsProstaglandin D2 receptor 2, Endolysin chimera
KeywordsMEMBRANE PROTEIN / prostaglandin D2 receptor / CRTH2 / 15R-methyl-PGD2 / G protein-coupled receptor / GPCR / Endolysin fusion / LCP
Function / homology
Function and homology information


prostaglandin J receptor activity / prostaglandin D receptor activity / prostaglandin F receptor activity / Prostanoid ligand receptors / negative regulation of male germ cell proliferation / positive regulation of G protein-coupled receptor signaling pathway / neuropeptide binding / neuropeptide signaling pathway / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway ...prostaglandin J receptor activity / prostaglandin D receptor activity / prostaglandin F receptor activity / Prostanoid ligand receptors / negative regulation of male germ cell proliferation / positive regulation of G protein-coupled receptor signaling pathway / neuropeptide binding / neuropeptide signaling pathway / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptidoglycan catabolic process / G protein-coupled receptor activity / calcium-mediated signaling / chemotaxis / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (i) signalling events / host cell cytoplasm / defense response to bacterium / neuron projection / 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 / Lysozyme domain superfamily / Phage lysozyme / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. ...Formyl peptide receptor-related / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
CITRATE ANION / 15R-methyl-prostaglandin D2 / Endolysin / Prostaglandin D2 receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsShiriaeva, A. / Han, G.W. / Cherezov, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Molecular basis for lipid recognition by the prostaglandin D 2 receptor CRTH2.
Authors: Liu, H. / Deepak, R.N.V.K. / Shiriaeva, A. / Gati, C. / Batyuk, A. / Hu, H. / Weierstall, U. / Liu, W. / Wang, L. / Cherezov, V. / Fan, H. / Zhang, C.
History
DepositionMar 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin D2 receptor 2, Endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2889
Polymers52,2291
Non-polymers1,0598
Water21612
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 67.800, 265.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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 D2 receptor 2, Endolysin chimera /


Mass: 52228.727 Da / Num. of mol.: 1
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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y5Y4, UniProt: D9IEF7

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Non-polymers , 5 types, 20 molecules

#2: Chemical ChemComp-YSS / 15R-methyl-prostaglandin D2 / (5Z,13E,15R,16E)-9alpha,15-dihydroxy-15-methyl-11-oxo-12alpha-prosta-5,13,16-trien-1-oic acid


Mass: 366.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20358

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Sample preparation

CrystalDensity Matthews: 4.43 Å3/Da / Density % sol: 72.22 %
Crystal growTemperature: 283 K / Method: lipidic cubic phase / pH: 6
Details: sodium chloride, lithium sulphate, sodium citrate tribasic dihydrate, PEG 300, propylene glycol P400, PGD2

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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: 1.33 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 4, 2018 / Frequency: 120
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 2.6→32.43 Å / Num. obs: 29269 / % possible obs: 98.9 % / Redundancy: 61.8 % / CC star: 0.99 / R split: 0.264 / Net I/σ(I): 2.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 12462 / CC star: 0.512 / R split: 5.14 / % possible all: 90.6
Serial crystallography measurementCollection time total: 2 hours / Collimation: KB mirrors / Focal spot size: 2 µm2 / Pulse duration: 35 fsec. / Pulse energy: 0.1 µJ / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Description: LCP injector / Flow rate: 0.44 µL/min / Injector diameter: 50 µm / Injector temperature: 293 K / Jet diameter: 50 µm / Power by: HPLC pump
Serial crystallography data reductionCrystal hits: 20358 / Frames total: 850000

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D27

6d27


Resolution: 2.61→32.43 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2669 781 4.99 %
Rwork0.2291 14861 -
obs0.2311 15642 53.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.54 Å2 / Biso mean: 52.3671 Å2 / Biso min: 10.52 Å2
Refinement stepCycle: final / Resolution: 2.61→32.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 65 12 3494
Biso mean--68.02 38.22 -
Num. residues----437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.61-2.770.4058270.3293854129
2.77-2.980.3855380.320565669415
2.98-3.280.2846600.2851274133428
3.28-3.760.29181540.26113021317565
3.76-4.730.2652450.207446594904100
4.73-32.430.24892570.223948665123100
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)
10.99510.3968-0.27811.1180.31450.2731-0.29880.7457-0.1656-1.33230.50460.59140.3432-0.01730.01460.77130.039-0.11430.72960.14120.5198-7.22-57.0611531.3694
22.3665-0.00240.90191.3469-0.442.8493-0.18560.03440.1083-0.03920.0860.0027-0.0401-0.1793-0.07520.07370.1420.0586-0.02710.07790.1838-1.8174-55.2577560.471
32.6415-0.3103-0.64751.99351.09242.3411-0.2472-0.2398-0.02410.36970.5209-0.55160.50730.78060.00850.42790.1452-0.12310.4541-0.13010.42699.1162-48.084597.9843
41.99990.18531.59161.8119-0.81992.2363-0.1445-0.0281-0.1024-0.10820.09610.26930.6089-0.4409-0.05550.2414-0.0969-0.07760.0610.13860.2866-10.966-61.662561.9317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 32 )A3 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 903 )A33 - 1241
3X-RAY DIFFRACTION3chain 'A' and (resid 904 through 244 )A904 - 244
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 330 )A245 - 330

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