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- PDB-6me8: XFEL crystal structure of human melatonin receptor MT2 (N86D) in ... -

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Basic information

Entry
Database: PDB / ID: 6me8
TitleXFEL crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin
ComponentsSoluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
KeywordsMEMBRANE PROTEIN / GPCR / melatonin receptor type 1B (MT2) / N86D mutation / 2-phenylmelatonin / XFEL / LCP / BRIL / Rubredoxin / circadian rhythm / jetlag / type 2 diabetes
Function / homology
Function and homology information


melatonin receptor activity / positive regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of transmission of nerve impulse / positive regulation of transmission of nerve impulse / regulation of neuronal action potential / alkane catabolic process / camera-type eye development / Class A/1 (Rhodopsin-like receptors) / negative regulation of receptor guanylyl cyclase signaling pathway / negative regulation of vasoconstriction ...melatonin receptor activity / positive regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of transmission of nerve impulse / positive regulation of transmission of nerve impulse / regulation of neuronal action potential / alkane catabolic process / camera-type eye development / Class A/1 (Rhodopsin-like receptors) / negative regulation of receptor guanylyl cyclase signaling pathway / negative regulation of vasoconstriction / negative regulation of cytosolic calcium ion concentration / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / regulation of insulin secretion / negative regulation of insulin secretion / electron transport chain / G protein-coupled receptor activity / glucose homeostasis / G alpha (i) signalling events / chemical synaptic transmission / negative regulation of neuron apoptotic process / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / heme binding / synapse / plasma membrane
Similarity search - Function
Melatonin receptor family / Melatonin receptor 1A/1B / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain ...Melatonin receptor family / Melatonin receptor 1A/1B / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Cytochrome c/b562 / Rubrerythrin, domain 2 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Single Sheet / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-JEY / Rubredoxin / Soluble cytochrome b562 / Melatonin receptor type 1B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJohansson, L.C. / Stauch, B. / McCorvy, J. / Han, G.W. / Patel, N. / Batyuk, A. / Gati, C. / Li, C. / Grandner, J. / Hao, S. ...Johansson, L.C. / Stauch, B. / McCorvy, J. / Han, G.W. / Patel, N. / Batyuk, A. / Gati, C. / Li, C. / Grandner, J. / Hao, S. / Olsen, R.H.J. / Tribo, A.R. / Zaare, S. / Zhu, L. / Zatsepin, N.A. / Weierstall, U. / Liu, W. / Roth, B.L. / Katritch, V. / 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: XFEL structures of the human MT2melatonin receptor reveal the basis of subtype selectivity.
Authors: Johansson, L.C. / Stauch, B. / McCorvy, J.D. / Han, G.W. / Patel, N. / Huang, X.P. / Batyuk, A. / Gati, C. / Slocum, S.T. / Li, C. / Grandner, J.M. / Hao, S. / Olsen, R.H.J. / Tribo, A.R. / ...Authors: Johansson, L.C. / Stauch, B. / McCorvy, J.D. / Han, G.W. / Patel, N. / Huang, X.P. / Batyuk, A. / Gati, C. / Slocum, S.T. / Li, C. / Grandner, J.M. / Hao, S. / Olsen, R.H.J. / Tribo, A.R. / Zaare, S. / Zhu, L. / Zatsepin, N.A. / Weierstall, U. / Yous, S. / Stevens, R.C. / Liu, W. / Roth, B.L. / Katritch, V. / 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 1.4Apr 29, 2020Group: 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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
B: Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7135
Polymers103,0312
Non-polymers6823
Water00
1
A: Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8893
Polymers51,5161
Non-polymers3742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8242
Polymers51,5161
Non-polymers3081
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.700, 145.800, 77.000
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin / Cytochrome b-562 / Mel1b receptor / Rd / Mel1b receptor


Mass: 51515.566 Da / Num. of mol.: 2
Mutation: M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: cybC, MTNR1B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0ABE7, UniProt: P49286, UniProt: P00268
#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.: 2 / Source method: obtained synthetically / Formula: C19H20N2O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate

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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: 3.1→22 Å / Num. obs: 26228 / % possible obs: 100 % / Redundancy: 133 % / Biso Wilson estimate: 76.61 Å2 / R split: 0.19 / Net I/σ(I): 3.87
Reflection shellResolution: 3.1→3.23 Å / Num. unique obs: 3025
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 pump
Serial crystallography data reductionCrystal hits: 22267 / Frames indexed: 20704 / Frames total: 293060

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB id:1IRO

1iro


Resolution: 3.1→22 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.876 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.327 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.937 / SU Rfree Blow DPI: 0.372 / SU Rfree Cruickshank DPI: 0.391
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1309 5 %RANDOM
Rwork0.234 ---
obs0.235 26179 100 %-
Displacement parametersBiso mean: 130.74 Å2
Baniso -1Baniso -2Baniso -3
1--53.7473 Å20 Å2-31.5378 Å2
2--49.5135 Å20 Å2
3---4.2338 Å2
Refine analyzeLuzzati coordinate error obs: 1.01 Å
Refinement stepCycle: 1 / Resolution: 3.1→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6045 0 47 0 6092
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096248HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.968608HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2644SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes958HARMONIC5
X-RAY DIFFRACTIONt_it6248HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion2.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion891SEMIHARMONIC5
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_contact7410SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.267 144 4.92 %
Rwork0.287 2785 -
all0.286 2929 -
obs--99.97 %

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