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- PDB-6me5: XFEL crystal structure of human melatonin receptor MT1 in complex... -

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Basic information

Entry
Database: PDB / ID: 6me5
TitleXFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine
Componentschimera protein of Melatonin receptor type 1A and GlgA glycogen synthase
KeywordsMEMBRANE PROTEIN / GPCR / melatonin receptor type 1A (MT1) / agomelatine / XFEL / LCP / PGS / circadian rhythm / jetlag
Function / homology
Function and homology information


melatonin receptor activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / Class A/1 (Rhodopsin-like receptors) / mating behavior / hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled receptor activity / circadian rhythm / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G alpha (i) signalling events ...melatonin receptor activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / Class A/1 (Rhodopsin-like receptors) / mating behavior / hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled receptor activity / circadian rhythm / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G alpha (i) signalling events / receptor complex / G protein-coupled receptor signaling pathway / plasma membrane
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-AWY / OLEIC ACID / Melatonin receptor type 1A / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsStauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Gati, C. / Batyuk, A. / Ishchenko, A. / Brehm, W. / White, T.A. ...Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Gati, C. / Batyuk, A. / Ishchenko, A. / Brehm, W. / White, T.A. / Michaelian, N. / Madsen, C. / Zhu, L. / Grant, T.D. / Grandner, J.M. / Olsen, R.H.J. / Tribo, A.R. / Weierstall, U. / Roth, B.L. / Katritch, V. / Liu, W. / Cherezov, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127026 United States
CitationJournal: Nature / Year: 2019
Title: Structural basis of ligand recognition at the human MT1melatonin receptor.
Authors: Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Huang, X.P. / Gati, C. / Batyuk, A. / Slocum, S.T. / Ishchenko, A. / Brehm, W. / White, T.A. / Michaelian, N. / Madsen, ...Authors: Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Huang, X.P. / Gati, C. / Batyuk, A. / Slocum, S.T. / Ishchenko, A. / Brehm, W. / White, T.A. / Michaelian, N. / Madsen, C. / Zhu, L. / Grant, T.D. / Grandner, J.M. / Shiriaeva, A. / Olsen, R.H.J. / Tribo, A.R. / Yous, S. / Stevens, R.C. / Weierstall, U. / Katritch, V. / Roth, B.L. / Liu, W. / Cherezov, V.
History
DepositionSep 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 3, 2021Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 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: chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1233
Polymers56,5971
Non-polymers5262
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, 122.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsAUTHORS STATE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein chimera 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 GE5 (archaea)
Gene: MTNR1A, PAB2292 / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P48039, UniProt: Q9V2J8
#2: Chemical ChemComp-AWY / ~{N}-[2-(7-methoxynaphthalen-1-yl)ethyl]ethanamide


Mass: 243.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2

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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: 4.05 Å3/Da / Density % sol: 69.63 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) 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: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 3.2→28.9 Å / Num. obs: 15917 / % possible obs: 100 % / Redundancy: 15917 % / Biso Wilson estimate: 64.1 Å2 / R split: 0.12 / Net I/σ(I): 8.7
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 151.6 % / Mean I/σ(I) obs: 0.7 / R split: 1.673 / % possible all: 100
Serial crystallography measurementPulse duration: 30 fsec. / Pulse energy: 3 µJ / Pulse photon energy: 9.83 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Flow rate: 0.357 µL/min / Injector diameter: 50 µm / Injector nozzle: LCP / Power by: HPLC
Serial crystallography data reductionCrystal hits: 45820 / Frames indexed: 43423 / Frames total: 466602

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
PHASER2.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S0V

4s0v


Resolution: 3.2→28.87 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.918 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.375 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 1.445 / SU Rfree Blow DPI: 0.391 / SU Rfree Cruickshank DPI: 0.396
RfactorNum. reflection% reflectionSelection details
Rfree0.257 797 5.03 %RANDOM
Rwork0.232 ---
obs0.234 15853 99.7 %-
Displacement parametersBiso mean: 114.65 Å2
Baniso -1Baniso -2Baniso -3
1--5.0291 Å20 Å20 Å2
2---5.0291 Å20 Å2
3---10.0582 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: 1 / Resolution: 3.2→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 37 0 3695
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093783HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.935159HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1667SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes569HARMONIC5
X-RAY DIFFRACTIONt_it3783HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.08
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion512SEMIHARMONIC5
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_contact4417SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.231 145 5.18 %
Rwork0.228 2653 -
all0.228 2798 -
obs--99.08 %

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