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- PDB-7yxa: XFEL crystal structure of the human sphingosine 1 phosphate recep... -

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Basic information

Entry
Database: PDB / ID: 7yxa
TitleXFEL crystal structure of the human sphingosine 1 phosphate receptor 5 in complex with ONO-5430608
ComponentsSphingosine 1-phosphate receptor 5,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / GPCR / g-protein coupled receptor / XFEL / X-ray free electron laser / serial femtosecond crystallography / SFX / sphingosine-1-phosphate / sphingosine-1-phosphate receptor / S1P5
Function / homology
Function and homology information


sphingosine-1-phosphate receptor activity / Lysosphingolipid and LPA receptors / regulation of metabolic process / regulation of neuron differentiation / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / membrane => GO:0016020 / periplasmic space ...sphingosine-1-phosphate receptor activity / Lysosphingolipid and LPA receptors / regulation of metabolic process / regulation of neuron differentiation / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / membrane => GO:0016020 / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane / cytoplasm
Similarity search - Function
EDG-8 sphingosine 1-phosphate receptor / Sphingosine 1-phosphate receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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-B2O / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Sphingosine 1-phosphate receptor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLyapina, E. / Marin, E. / Gusach, A. / Orekhov, P. / Gerasimov, A. / Luginina, A. / Vakhrameev, D. / Ergasheva, M. / Kovaleva, M. / Khusainov, G. ...Lyapina, E. / Marin, E. / Gusach, A. / Orekhov, P. / Gerasimov, A. / Luginina, A. / Vakhrameev, D. / Ergasheva, M. / Kovaleva, M. / Khusainov, G. / Khorn, P. / Shevtsov, M. / Kovalev, K. / Okhrimenko, I. / Bukhdruker, S. / Popov, P. / Hu, H. / Weierstall, U. / Liu, W. / Cho, Y. / Gushchin, I. / Rogachev, A. / Bourenkov, G. / Park, S. / Park, G. / Huyn, H.J. / Park, J. / Gordeliy, V. / Borshchevskiy, V. / Mishin, A. / Cherezov, V.
Funding support Russian Federation, Korea, Republic Of, 4items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00261 Russian Federation
Russian Foundation for Basic Research18-02-40020 Russian Federation
Ministry of Science and Higher Education of the Russian Federationagreement # 075-00337-20-03, project FSMG-2020-0003 Russian Federation
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for receptor selectivity and inverse agonism in S1P 5 receptors.
Authors: Lyapina, E. / Marin, E. / Gusach, A. / Orekhov, P. / Gerasimov, A. / Luginina, A. / Vakhrameev, D. / Ergasheva, M. / Kovaleva, M. / Khusainov, G. / Khorn, P. / Shevtsov, M. / Kovalev, K. / ...Authors: Lyapina, E. / Marin, E. / Gusach, A. / Orekhov, P. / Gerasimov, A. / Luginina, A. / Vakhrameev, D. / Ergasheva, M. / Kovaleva, M. / Khusainov, G. / Khorn, P. / Shevtsov, M. / Kovalev, K. / Bukhdruker, S. / Okhrimenko, I. / Popov, P. / Hu, H. / Weierstall, U. / Liu, W. / Cho, Y. / Gushchin, I. / Rogachev, A. / Bourenkov, G. / Park, S. / Park, G. / Hyun, H.J. / Park, J. / Gordeliy, V. / Borshchevskiy, V. / Mishin, A. / Cherezov, V.
History
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 2.0Aug 17, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num
Revision 2.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.3Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 2.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingosine 1-phosphate receptor 5,Soluble cytochrome b562
B: Sphingosine 1-phosphate receptor 5,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,73111
Polymers99,8452
Non-polymers2,8869
Water3,495194
1
A: Sphingosine 1-phosphate receptor 5,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6186
Polymers49,9231
Non-polymers1,6955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sphingosine 1-phosphate receptor 5,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1135
Polymers49,9231
Non-polymers1,1914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.840, 103.420, 187.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Sphingosine 1-phosphate receptor 5,Soluble cytochrome b562 / S1P receptor 5 / S1P5 / Endothelial differentiation G-protein-coupled receptor 8 / Sphingosine 1- ...S1P receptor 5 / S1P5 / Endothelial differentiation G-protein-coupled receptor 8 / Sphingosine 1-phosphate receptor Edg-8 / S1P receptor Edg-8 / Cytochrome b-562


Mass: 49922.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S1PR5, EDG8, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H228, UniProt: P0ABE7
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 201 molecules

#3: Chemical ChemComp-B2O / 4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid


Mass: 404.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H30NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.48 % / Description: crystal size less than 10 um
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 7
Details: crystallization in syringes in precipitant conditions containing 100-300 mM KH2PO4 monobasic, 28-32% v/v PEG400, and 100 mM HEPES pH 7
Temp details: 20-23 Celcius

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Data collection

DiffractionMean temperature: 296 K / Ambient temp details: helium chamber, 1 atm / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.278 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 7, 2019 / Frequency: 30
RadiationMonochromator: pair of Kirkpatrick-Baez mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 60071 / % possible obs: 99.93 % / Redundancy: 119.3 % / Biso Wilson estimate: 30.21 Å2 / CC1/2: 0.92 / CC star: 0.979 / R split: 0.244 / Net I/σ(I): 3.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 112 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5883 / CC1/2: 0.154 / CC star: 0.516 / R split: 0.718 / % possible all: 100
Serial crystallography measurementFocal spot size: 6 µm2 / Pulse duration: 25 fsec. / Pulse photon energy: 9700 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: LCP injector / Method: injection
Serial crystallography sample delivery injectionDescription: LCP injector / Flow rate: 0.15 µL/min / Injector diameter: 50 µm / Injector temperature: 296 K
Serial crystallography data reductionCrystal hits: 6918 / Frames indexed: 6918 / Frames total: 490000 / Lattices indexed: 7492 / XFEL pulse events: 490000

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
CrystFEL0.8.0data reduction
CrystFEL0.10.1data scaling
PHASER1.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3v2y, 4eiy

3v2y

4eiy


Resolution: 2.2→29.97 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3292 1999 3.33 %
Rwork0.3007 58072 -
obs0.3017 60071 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.33 Å2 / Biso mean: 48.9206 Å2 / Biso min: 3.1 Å2
Refinement stepCycle: final / Resolution: 2.2→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 414 194 6189
Biso mean--49.23 40.81 -
Num. residues----748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.250.38561400.376740524192
2.26-2.320.40331410.348841024243
2.32-2.380.32631410.328641014242
2.38-2.460.36281400.327740724212
2.46-2.550.38011410.327240994240
2.55-2.650.36191430.327541334276
2.65-2.770.38121410.323441014242
2.77-2.920.35381420.295741324274
2.92-3.10.29631420.284241234265
3.1-3.340.30761430.275441664309
3.34-3.670.31081420.263641454287
3.67-4.210.2881450.245941914336
4.21-5.290.2871450.279742314376
5.29-29.970.34811530.336944244577
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)
10.2913-0.06430.02750.31020.03910.6987-0.0020.1029-0.0152-0.2351-0.0367-0.0765-0.1077-0.0393-0.08630.3311-0.00130.14370.12970.25760.218819.195618.8349-10.1068
20.3889-0.20540.27810.1873-0.03440.41520.03050.04-0.1137-0.11060.06640.1007-0.14490.0031-0.10660.34550.00530.11310.4718-0.18820.403711.9162-18.878811.5946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and (resid 6 through 413))A6 - 413
2X-RAY DIFFRACTION2(chain 'B' and (resid 12 through 413))B12 - 413

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