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- PDB-6wh4: Crystal structure of HTR2A with inverse agonist -

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Basic information

Entry
Database: PDB / ID: 6wh4
TitleCrystal structure of HTR2A with inverse agonist
Components5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion
KeywordsMEMBRANE PROTEIN / HTR2A
Function / homology
Function and homology information


protein localization to cytoskeleton / positive regulation of heat generation / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / neurofilament / cell body fiber / phospholipase C-activating serotonin receptor signaling pathway ...protein localization to cytoskeleton / positive regulation of heat generation / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / neurofilament / cell body fiber / phospholipase C-activating serotonin receptor signaling pathway / artery smooth muscle contraction / Serotonin receptors / serotonin receptor activity / positive regulation of cytokine production involved in immune response / G protein-coupled serotonin receptor activity / sensitization / serotonin receptor signaling pathway / neurotransmitter receptor activity / urinary bladder smooth muscle contraction / serotonin binding / positive regulation of platelet aggregation / negative regulation of synaptic transmission, glutamatergic / positive regulation of DNA biosynthetic process / temperature homeostasis / positive regulation of vasoconstriction / detection of temperature stimulus involved in sensory perception of pain / regulation of dopamine secretion / negative regulation of potassium ion transport / protein tyrosine kinase activator activity / positive regulation of execution phase of apoptosis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of fat cell differentiation / behavioral response to cocaine / release of sequestered calcium ion into cytosol / presynaptic modulation of chemical synaptic transmission / positive regulation of glycolytic process / dendritic shaft / glycolytic process / electron transport chain / caveola / memory / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of neuron apoptotic process / positive regulation of cytosolic calcium ion concentration / virus receptor activity / presynaptic membrane / cytoplasmic vesicle / G alpha (q) signalling events / chemical synaptic transmission / postsynaptic membrane / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / iron ion binding / response to xenobiotic stimulus / axon / neuronal cell body / positive regulation of cell population proliferation / heme binding / dendrite / protein-containing complex binding / glutamatergic synapse / 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-89F / CHOLESTEROL / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE / OLEIC ACID / DI(HYDROXYETHYL)ETHER / 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 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)155,43618
Polymers151,6053
Non-polymers3,83115
Water00
1
A: 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9496
Polymers50,5351
Non-polymers1,4145
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)51,2804
Polymers50,5351
Non-polymers7453
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)52,2068
Polymers50,5351
Non-polymers1,6717
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.380, 177.310, 280.590
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, 15 molecules

#2: Chemical ChemComp-89F / 1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine / Methiothepin / Metitepine


Mass: 356.548 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H24N2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NDS / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE


Mass: 195.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3S
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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
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: 3.79 Å3/Da / Density % sol: 67.55 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7
Details: 100 mM Tris (pH7.0) 380 mM potassium phosphate-monobasic 33% PEG 400 100 mM Guanidine HCL 300 mM NDSB-195

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 3→34.78 Å / Num. obs: 41269 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 65.18 Å2 / CC1/2: 0.994 / Net I/σ(I): 4.2
Reflection shellResolution: 3→3.12 Å / Num. unique obs: 4468 / CC1/2: 0.306

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Processing

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

5tvn


Resolution: 3.4→33.5 Å / SU ML: 0.4708 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.5739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3037 1336 5.12 %
Rwork0.2581 24760 -
obs0.2604 26096 90.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.64 Å2
Refinement stepCycle: LAST / Resolution: 3.4→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7863 0 245 0 8108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01178258
X-RAY DIFFRACTIONf_angle_d1.501511302
X-RAY DIFFRACTIONf_chiral_restr0.07141400
X-RAY DIFFRACTIONf_plane_restr0.00911378
X-RAY DIFFRACTIONf_dihedral_angle_d15.41161337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.520.3275630.29351176X-RAY DIFFRACTION44.09
3.52-3.660.3221890.29341826X-RAY DIFFRACTION67.72
3.66-3.830.33951420.2712579X-RAY DIFFRACTION95.98
3.83-4.030.33711460.25372709X-RAY DIFFRACTION100
4.03-4.280.3081530.24672685X-RAY DIFFRACTION99.96
4.28-4.610.27161650.23062708X-RAY DIFFRACTION100
4.61-5.070.28921400.232714X-RAY DIFFRACTION99.76
5.07-5.810.26131400.26762741X-RAY DIFFRACTION99.83
5.81-7.30.35951620.32592745X-RAY DIFFRACTION100
7.3-33.50.281360.24622877X-RAY DIFFRACTION99.28

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