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- PDB-5v54: Crystal structure of 5-HT1B receptor in complex with methiothepin -

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Basic information

Entry
Database: PDB / ID: 5v54
TitleCrystal structure of 5-HT1B receptor in complex with methiothepin
Components5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1b receptor,5-hydroxytryptamine receptor 1B
KeywordsELECTRON TRANSPORT / 5-hydroxytryptamine / GPCR antagonist / OB1
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / adenylate cyclase-inhibiting serotonin receptor signaling pathway / negative regulation of gamma-aminobutyric acid secretion / G protein-coupled serotonin receptor complex / serotonergic synapse / regulation of behavior / Serotonin receptors / negative regulation of synaptic transmission, GABAergic / response to mineralocorticoid / negative regulation of serotonin secretion ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / adenylate cyclase-inhibiting serotonin receptor signaling pathway / negative regulation of gamma-aminobutyric acid secretion / G protein-coupled serotonin receptor complex / serotonergic synapse / regulation of behavior / Serotonin receptors / negative regulation of synaptic transmission, GABAergic / response to mineralocorticoid / negative regulation of serotonin secretion / drinking behavior / cellular response to temperature stimulus / serotonin binding / bone remodeling / negative regulation of synaptic transmission, glutamatergic / G protein-coupled serotonin receptor activity / vasoconstriction / protein kinase C-activating G protein-coupled receptor signaling pathway / neurotransmitter receptor activity / G protein-coupled receptor internalization / regulation of synaptic vesicle exocytosis / regulation of dopamine secretion / heterocyclic compound binding / cellular response to alkaloid / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / calyx of Held / positive regulation of vascular associated smooth muscle cell proliferation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / presynaptic modulation of chemical synaptic transmission / response to cocaine / cellular response to xenobiotic stimulus / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / response to ethanol / dendrite / endoplasmic reticulum / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 1B receptor / 5-hydroxytryptamine receptor family / 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-89F / 5-hydroxytryptamine receptor 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Spodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsYin, W.C. / Zhou, X.E. / Yang, D. / de Waal, P. / Wang, M.T. / Dai, A. / Cai, X. / Huang, C.Y. / Liu, P. / Yin, Y. ...Yin, W.C. / Zhou, X.E. / Yang, D. / de Waal, P. / Wang, M.T. / Dai, A. / Cai, X. / Huang, C.Y. / Liu, P. / Yin, Y. / Liu, B. / Caffrey, M. / Melcher, K. / Xu, Y. / Wang, M.W. / Xu, H.E. / Jiang, Y.
Funding support China, United States, 16items
OrganizationGrant numberCountry
National Natural Science Foundation31300607 China
Outstanding Young Scientist Foundation China
Jay and Betty Van Andel Foundation United States
Ministry of Science and Technology of China2012ZX09301001 China
Ministry of Science and Technology of China2012CB910403 China
Ministry of Science and Technology of China2013CB9106010 China
Ministry of Science and Technology of ChinaXDB08020303 China
Ministry of Science and Technology of China2013ZX09507001 China
National Institutes of HealthDK071662 United States
National Institutes of HealthGM102545 United States
National Institutes of HealthGM104212 United States
Shanghai Science and Technology Development Fund15DZ2291600 China
Shanghai Science and Technology Development Fund14431901200 China
National Natural Science Foundation81373463 China
CAS-Novo Nordisk Research Fund China
Youth Innovation Promotion Association of CAS China
CitationJournal: Cell Discov / Year: 2018
Title: A common antagonistic mechanism for class A GPCRs revealed by the structure of the human 5-HT1B serotonin receptor bound to an antagonist
Authors: Yin, W.C. / Zhou, X.E. / Yang, D. / De Waal, P. / Wang, M.T. / Dai, A. / Cai, X. / Huang, C.Y. / Liu, P. / Yin, Y. / Liu, B. / Caffrey, M. / Melcher, K. / Xu, Y. / Wang, M.W. / Xu, H.E. / Jiang, Y.
History
DepositionMar 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1b receptor,5-hydroxytryptamine receptor 1B
B: 5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1b receptor,5-hydroxytryptamine receptor 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6434
Polymers89,9302
Non-polymers7132
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-24 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.200, 48.830, 139.220
Angle α, β, γ (deg.)90.00, 124.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1b receptor,5-hydroxytryptamine receptor 1B / 5-HT1B / S12 / Serotonin 1D beta receptor / 5-HT-1D-beta / Serotonin receptor 1B


Mass: 44965.156 Da / Num. of mol.: 2 / Fragment: UNP residues 37-239,UNP residues 304-390 / Mutation: L138W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Spodoptera frugiperda (fall armyworm)
Gene: HTR1B, HTR1DB / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28222
#2: Chemical ChemComp-89F / 1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine / Methiothepin, Metitepine / Metitepine


Mass: 356.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N2S2 / Comment: antipsychotic, antagonist*YM

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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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100mM Bis-Tris (pH7.0), 155mM Ammonium phosphate monobasic, 26% PEG300, 0.01M GSH (L-Glutathione reduced), GSSG (L-Glutathione oxidized)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→45.5 Å / Num. obs: 12888 / % possible obs: 95.9 % / Redundancy: 7.2 % / Net I/σ(I): 4.37

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→45.506 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2881 857 7.14 %
Rwork0.272 --
obs0.2728 11996 96.73 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.9→45.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 48 0 6180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066332
X-RAY DIFFRACTIONf_angle_d1.0978627
X-RAY DIFFRACTIONf_dihedral_angle_d12.3622283
X-RAY DIFFRACTIONf_chiral_restr0.0431009
X-RAY DIFFRACTIONf_plane_restr0.0061056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9001-4.03940.4278710.4211984X-RAY DIFFRACTION85
4.0394-4.20110.4082980.40491041X-RAY DIFFRACTION94
4.2011-4.39210.4284850.35441110X-RAY DIFFRACTION98
4.3921-4.62350.3516740.311140X-RAY DIFFRACTION99
4.6235-4.91280.2857910.27331104X-RAY DIFFRACTION97
4.9128-5.29160.2869820.29231101X-RAY DIFFRACTION97
5.2916-5.82320.2841860.27711129X-RAY DIFFRACTION99
5.8232-6.66350.29321010.28711145X-RAY DIFFRACTION99
6.6635-8.38680.2875910.24711164X-RAY DIFFRACTION100
8.3868-45.50940.2177780.22241221X-RAY DIFFRACTION99

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