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- PDB-6wgt: Crystal structure of HTR2A with hallucinogenic agonist -

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Basic information

Entry
Database: PDB / ID: 6wgt
TitleCrystal structure of HTR2A with hallucinogenic agonist
Components5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion
KeywordsMEMBRANE PROTEIN / HTR2A
Function / homology
Function and homology information


protein localization to cytoskeleton / 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 / serotonin receptor signaling pathway / Serotonin receptors / artery smooth muscle contraction ...protein localization to cytoskeleton / 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 / serotonin receptor signaling pathway / Serotonin receptors / artery smooth muscle contraction / cell body fiber / urinary bladder smooth muscle contraction / serotonin binding / negative regulation of synaptic transmission, glutamatergic / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / temperature homeostasis / regulation of dopamine secretion / protein tyrosine kinase activator activity / behavioral response to cocaine / detection of temperature stimulus involved in sensory perception of pain / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / negative regulation of potassium ion transport / activation of phospholipase C activity / positive regulation of fat cell differentiation / detection of mechanical stimulus involved in sensory perception of pain / release of sequestered calcium ion into cytosol / positive regulation of vasoconstriction / presynaptic modulation of chemical synaptic transmission / positive regulation of glycolytic process / dendritic shaft / phosphatidylinositol 3-kinase/protein kinase B signal transduction / caveola / glycolytic process / intracellular calcium ion homeostasis / memory / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / cytoplasmic vesicle / postsynaptic membrane / G alpha (q) signalling events / electron transfer activity / periplasmic space / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / iron ion binding / axon / dendrite / neuronal cell body / glutamatergic synapse / positive regulation of cell population proliferation / heme binding / protein-containing complex binding / identical protein binding / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 2A 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-7LD / CHOLESTEROL / OLEIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Soluble cytochrome b562 / 5-hydroxytryptamine receptor 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKim, K.L. / Che, T. / Krumm, B.E. / Roth, B.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R37 DA045657 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1 MH112205 United States
CitationJournal: Cell(Cambridge,Mass.) / Year: 2020
Title: Structure of a Hallucinogen-Activated Gq-Coupled 5-HT 2A Serotonin Receptor
Authors: Kim, K.L. / Che, T. / Panova, O. / DiBerto, J.F. / Lyu, J. / Krumm, B.E. / Wacker, D. / Robertson, M.J. / Seven, A.B. / Nichols, D.E. / Shoichet, B.K. / Skiniotis, G. / Roth, B.L.
History
DepositionApr 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)154,93117
Polymers151,6053
Non-polymers3,32614
Water0
1
A: 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3037
Polymers50,5351
Non-polymers1,7686
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3315
Polymers50,5351
Non-polymers7964
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2985
Polymers50,5351
Non-polymers7634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.640, 175.260, 280.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion / 5-HT-2A / Serotonin receptor 2A / Cytochrome b-562


Mass: 50534.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: HTR2A, HTR2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28223, UniProt: P0ABE7

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Non-polymers , 6 types, 14 molecules

#2: Chemical ChemComp-7LD / (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide / Lysergic acid diethylamide / Lysergic acid diethylamide


Mass: 323.432 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H25N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM

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Details

Has ligand of interestY

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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: 3.71 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7
Details: 100 mM Tris (pH7.0) 370-410 mM KPO4-mono 90-120 mM GuHCl 28-34% PEG 400
PH range: 7.0 - 7.3

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.4→39.54 Å / Num. obs: 26609 / % possible obs: 94.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 67.57 Å2 / CC1/2: 0.97 / Net I/σ(I): 5.5
Reflection shellResolution: 3.4→3.63 Å / Num. unique obs: 3887 / CC1/2: 0.611 / % possible all: 77.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TVN

5tvn


Resolution: 3.4→34.54 Å / SU ML: 0.5716 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.7301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3054 1350 5.09 %
Rwork0.2648 25189 -
obs0.2669 26539 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.37 Å2
Refinement stepCycle: LAST / Resolution: 3.4→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7880 0 220 0 8100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01278257
X-RAY DIFFRACTIONf_angle_d1.494311298
X-RAY DIFFRACTIONf_chiral_restr0.08811397
X-RAY DIFFRACTIONf_plane_restr0.00911374
X-RAY DIFFRACTIONf_dihedral_angle_d14.70191270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.520.3898880.34231994X-RAY DIFFRACTION75.24
3.52-3.660.37241260.30942152X-RAY DIFFRACTION82.3
3.66-3.830.30591310.28092487X-RAY DIFFRACTION94.1
3.83-4.030.3421480.2642589X-RAY DIFFRACTION97.54
4.03-4.280.34021370.25492607X-RAY DIFFRACTION99.06
4.28-4.610.26111410.22322651X-RAY DIFFRACTION98.97
4.61-5.080.30991450.23652635X-RAY DIFFRACTION99.32
5.08-5.810.35031360.27762663X-RAY DIFFRACTION99.11
5.81-7.30.30351400.31292676X-RAY DIFFRACTION98.77
7.3-34.540.24881580.24192735X-RAY DIFFRACTION97.34

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