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- PDB-6bqh: Crystal structure of 5-HT2C in complex with ritanserin -

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Basic information

Entry
Database: PDB / ID: 6bqh
TitleCrystal structure of 5-HT2C in complex with ritanserin
Components5-hydroxytryptamine receptor 2C,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / human 5-HT2C receptor / GPCR / ritanserin / selectivity / BRIL / LCP
Function / homology
Function and homology information


regulation of corticotropin-releasing hormone secretion / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / regulation of appetite / regulation of nervous system process / Serotonin receptors ...regulation of corticotropin-releasing hormone secretion / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / regulation of appetite / regulation of nervous system process / Serotonin receptors / serotonin binding / G protein-coupled serotonin receptor activity / feeding behavior / neurotransmitter receptor activity / cGMP-mediated signaling / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / behavioral fear response / positive regulation of fat cell differentiation / positive regulation of calcium-mediated signaling / release of sequestered calcium ion into cytosol / locomotory behavior / electron transport chain / intracellular calcium ion homeostasis / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / chemical synaptic transmission / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / iron ion binding / synapse / dendrite / heme binding / identical protein binding / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 2C receptor / 5-hydroxytryptamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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-E2J / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Soluble cytochrome b562 / 5-hydroxytryptamine receptor 2C
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPeng, Y. / McCorvy, J.D. / Harpsoe, K. / Lansu, K. / Yuan, S. / Popov, P. / Qu, L. / Pu, M. / Che, T. / Nikolajse, L.F. ...Peng, Y. / McCorvy, J.D. / Harpsoe, K. / Lansu, K. / Yuan, S. / Popov, P. / Qu, L. / Pu, M. / Che, T. / Nikolajse, L.F. / Huang, X.P. / Wu, Y. / Shen, L. / Bjorn-Yoshimoto, W.E. / Ding, K. / Wacker, D. / Han, G.W. / Cheng, J. / Katritch, V. / Jensen, A.A. / Hanson, M.A. / Zhao, S. / Gloriam, D.E. / Roth, B.L. / Stevens, R.C. / Liu, Z.
CitationJournal: Cell / Year: 2018
Title: 5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology.
Authors: Peng, Y. / McCorvy, J.D. / Harpsoe, K. / Lansu, K. / Yuan, S. / Popov, P. / Qu, L. / Pu, M. / Che, T. / Nikolajsen, L.F. / Huang, X.P. / Wu, Y. / Shen, L. / Bjorn-Yoshimoto, W.E. / Ding, K. ...Authors: Peng, Y. / McCorvy, J.D. / Harpsoe, K. / Lansu, K. / Yuan, S. / Popov, P. / Qu, L. / Pu, M. / Che, T. / Nikolajsen, L.F. / Huang, X.P. / Wu, Y. / Shen, L. / Bjorn-Yoshimoto, W.E. / Ding, K. / Wacker, D. / Han, G.W. / Cheng, J. / Katritch, V. / Jensen, A.A. / Hanson, M.A. / Zhao, S. / Gloriam, D.E. / Roth, B.L. / Stevens, R.C. / Liu, Z.J.
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: 5-hydroxytryptamine receptor 2C,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,59811
Polymers51,3101
Non-polymers3,28810
Water724
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.310, 97.050, 150.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
DetailsAuthors state that the biological unit is unknown

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 5-hydroxytryptamine receptor 2C,Soluble cytochrome b562 / 5-HTR2C / 5-hydroxytryptamine receptor 1C / 5-HT1C / Serotonin receptor 2C / Cytochrome b-562


Mass: 51310.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: HTR2C, HTR1C, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28335, UniProt: P0ABE7

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Non-polymers , 5 types, 14 molecules

#2: Chemical ChemComp-E2J / 6-(2-{4-[bis(4-fluorophenyl)methylidene]piperidin-1-yl}ethyl)-7-methyl-5H-[1,3]thiazolo[3,2-a]pyrimidin-5-one / Ritanserin / Ritanserin


Mass: 477.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C27H25F2N3OS / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antidepressant, antagonist*YM
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 M sodium citrate pH 6.0, 100mM (NH4)2SO4, 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 17076 / % possible obs: 94.2 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.7 % / Num. unique obs: 1578 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2289: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IB4

4ib4


Resolution: 2.7→48.525 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.8
RfactorNum. reflection% reflection
Rfree0.2745 856 5.02 %
Rwork0.2531 --
obs0.2542 17052 94.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 154 4 2815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032863
X-RAY DIFFRACTIONf_angle_d0.63874
X-RAY DIFFRACTIONf_dihedral_angle_d12.9721706
X-RAY DIFFRACTIONf_chiral_restr0.039463
X-RAY DIFFRACTIONf_plane_restr0.004466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.86920.43011380.37982511X-RAY DIFFRACTION89
2.8692-3.09070.3911350.32412553X-RAY DIFFRACTION91
3.0907-3.40170.3821360.29192624X-RAY DIFFRACTION92
3.4017-3.89370.27861370.23592740X-RAY DIFFRACTION96
3.8937-4.90490.22461500.22352823X-RAY DIFFRACTION98
4.9049-48.53280.26481600.2522945X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 40.4427 Å / Origin y: 33.1211 Å / Origin z: 40.8027 Å
111213212223313233
T0.8265 Å2-0.0672 Å2-0.0406 Å2-0.8279 Å2-0.0198 Å2--0.8205 Å2
L2.5809 °2-0.1185 °2-0.7173 °2-1.326 °20.4424 °2--1.6583 °2
S-0.0695 Å °0.4302 Å °-0.1584 Å °-0.0728 Å °-0.0775 Å °0.0665 Å °0.1606 Å °0.0287 Å °0 Å °
Refinement TLS groupSelection details: all

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