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- PDB-6bqg: Crystal structure of 5-HT2C in complex with ergotamine -

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Basic information

Entry
Database: PDB / ID: 6bqg
TitleCrystal structure of 5-HT2C in complex with ergotamine
Components5-hydroxytryptamine receptor 2C,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / human 5-HT2C receptor / GPCR / ergotamine / polypharmacology / 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 / regulation of appetite / G protein-coupled serotonin receptor complex / 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 / regulation of appetite / G protein-coupled serotonin receptor complex / regulation of nervous system process / Serotonin receptors / serotonin receptor signaling pathway / 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 / positive regulation of fat cell differentiation / behavioral fear response / release of sequestered calcium ion into cytosol / positive regulation of calcium-mediated signaling / locomotory behavior / electron transport chain / intracellular calcium ion homeostasis / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / iron ion binding / dendrite / heme binding / synapse / 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
Ergotamine / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 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: 3 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
Revision 1.3Oct 30, 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: 5-hydroxytryptamine receptor 2C,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2483
Polymers51,3101
Non-polymers9382
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.840, 94.580, 145.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#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 / Mutation: M29W, H124I, R128L, C360N
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
#2: Chemical ChemComp-ERM / Ergotamine


Mass: 581.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35N5O5 / Comment: neurotransmitter, alkaloid*YM
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
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: 3.33 Å3/Da / Density % sol: 63.11 %
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: 3→50 Å / Num. obs: 12052 / % possible obs: 83.4 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.6
Reflection shellResolution: 3→3.1 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 5 / Num. unique obs: 943 / CC1/2: 0.9 / % possible all: 67.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IB4

4ib4


Resolution: 3→47.29 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2909 550 4.58 %
Rwork0.2612 --
obs0.2627 12007 83.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 54 0 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033098
X-RAY DIFFRACTIONf_angle_d0.5154221
X-RAY DIFFRACTIONf_dihedral_angle_d10.9351836
X-RAY DIFFRACTIONf_chiral_restr0.037501
X-RAY DIFFRACTIONf_plane_restr0.003516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.30190.4618850.44182298X-RAY DIFFRACTION68
3.3019-3.77960.37731260.33822651X-RAY DIFFRACTION79
3.7796-4.76110.26141510.24253095X-RAY DIFFRACTION91
4.7611-47.29590.27051880.22853413X-RAY DIFFRACTION96

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