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- PDB-6ps8: XFEL MT1R structure by ligand exchange from agomelatine to 2-phen... -

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Basic information

Entry
Database: PDB / ID: 6ps8
TitleXFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin.
ComponentsFusion protein of Melatonin receptor type 1A and GlgA glycogen synthase
KeywordsMEMBRANE PROTEIN / GPCR / COMPLEX-LCP method / SBDD / drug design / XFEL / LCP-SFX / Ligand Exchange / Agomelatine / 2-phenyl melatonin / MT1
Function / homology
Function and homology information


melatonin receptor activity / glycogen (starch) synthase activity / organic cyclic compound binding / hormone binding / Class A/1 (Rhodopsin-like receptors) / glycogen biosynthetic process / mating behavior / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity ...melatonin receptor activity / glycogen (starch) synthase activity / organic cyclic compound binding / hormone binding / Class A/1 (Rhodopsin-like receptors) / glycogen biosynthetic process / mating behavior / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / circadian rhythm / G alpha (i) signalling events / receptor complex / G protein-coupled receptor signaling pathway / plasma membrane / cytosol
Similarity search - Function
Melatonin receptor family / Melatonin receptor 1A/1B / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Melatonin receptor family / Melatonin receptor 1A/1B / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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-JEY / Melatonin receptor type 1A / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsIshchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N.A. / Weierstall, U. / Liu, W. / Nango, E. ...Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N.A. / Weierstall, U. / Liu, W. / Nango, E. / Nakane, T. / Tanaka, R. / Tono, K. / Joti, Y. / Iwata, S. / Moraes, I. / Gati, C. / Cherezov, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127086 United States
CitationJournal: Iucrj / Year: 2019
Title: Toward G protein-coupled receptor structure-based drug design using X-ray lasers.
Authors: Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N. / Weierstall, U. / Liu, W. / Nango, E. / Nakane, T. / Tanaka, R. / Tono, K. / Joti, Y. / Iwata, S. ...Authors: Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N. / Weierstall, U. / Liu, W. / Nango, E. / Nakane, T. / Tanaka, R. / Tono, K. / Joti, Y. / Iwata, S. / Moraes, I. / Gati, C. / Cherezov, V.
History
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

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Assembly

Deposited unit
A: Fusion protein of Melatonin receptor type 1A and GlgA glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9062
Polymers56,5971
Non-polymers3081
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.200, 122.200, 122.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Fusion protein of Melatonin receptor type 1A and GlgA glycogen synthase / Mel1a receptor / Glycogen synthase / Mel1a receptor


Mass: 56597.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: MTNR1A, PAB2292 / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P48039, UniProt: Q9V2J8
#2: Chemical ChemComp-JEY / N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide / 2-phenylmelatonin


Mass: 308.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
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: 4.04 Å3/Da / Density % sol: 69.58 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 60-100 mM potassium phosphate monobasic, 100 mM HEPES pH 7.0, 32-35% PEG 400, 1 mM of target ligand 2-phenylmelatonin, 2.5% DMSO, 1.5% propan-2-ol.

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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 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 14561 / % possible obs: 100 % / Redundancy: 1663 % / CC1/2: 0.998 / R split: 0.119 / Net I/σ(I): 8.5
Reflection shellResolution: 3.3→3.39 Å / Num. unique obs: 1109 / CC1/2: 0.163 / R split: 3.44
Serial crystallography measurementCollection time total: 2.27 hours / Focal spot size: 1.5 µm2 / Pulse duration: 35 fsec. / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionFlow rate: 0.2 µL/min / Injector diameter: 50 µm
Serial crystallography data reductionCrystal hits: 87453 / Frames indexed: 65260 / Frames total: 977748

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHASERphasing
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6me5

6me5


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.9 / SU B: 83.123 / SU ML: 0.542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.533
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3075 728 5 %RANDOM
Rwork0.2585 ---
obs0.2609 13778 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 201.26 Å2 / Biso mean: 114.238 Å2 / Biso min: 89.21 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å20 Å2
2---2.39 Å20 Å2
3---4.79 Å2
Refinement stepCycle: final / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 23 0 3671
Biso mean--107.44 --
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193760
X-RAY DIFFRACTIONr_bond_other_d0.0010.023456
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9625133
X-RAY DIFFRACTIONr_angle_other_deg0.90737900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.622.993137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77215546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8411517
X-RAY DIFFRACTIONr_chiral_restr0.0590.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
LS refinement shellResolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.607 54 -
Rwork0.507 984 -
all-1038 -
obs--100 %
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)
10.79990.06760.54211.8299-0.72594.0330.1535-0.1196-0.12320.0419-0.0099-0.01110.25390.2556-0.14360.8163-0.19-0.04310.7628-0.03580.024521.1537-26.908536.5854
23.31952.23890.19728.90751.6163.29060.0662-0.03460.4690.251-0.0778-0.109-0.0225-0.09770.01160.38420.0294-0.02140.33910.01810.336430.97242.26850.3633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 218
2X-RAY DIFFRACTION1A228 - 321
3X-RAY DIFFRACTION1A1201
4X-RAY DIFFRACTION2A1001 - 1196

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