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- PDB-5tvn: Crystal structure of the LSD-bound 5-HT2B receptor -

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Basic information

Entry
Database: PDB / ID: 5tvn
TitleCrystal structure of the LSD-bound 5-HT2B receptor
ComponentsChimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / LSD / GPCR / serotonin receptor
Function / homology
Function and homology information


behavior / intestine smooth muscle contraction / 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 / protein kinase C signaling / regulation of behavior / Serotonin receptors ...behavior / intestine smooth muscle contraction / 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 / protein kinase C signaling / regulation of behavior / Serotonin receptors / cellular response to temperature stimulus / embryonic morphogenesis / serotonin binding / 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 / cardiac muscle hypertrophy / neural crest cell differentiation / neural crest cell migration / cGMP-mediated signaling / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of cell division / activation of phospholipase C activity / G-protein alpha-subunit binding / heart morphogenesis / release of sequestered calcium ion into cytosol / ERK1 and ERK2 cascade / positive regulation of endothelial cell proliferation / GTPase activator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / positive regulation of cytokine production / positive regulation of MAP kinase activity / intracellular calcium ion homeostasis / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / positive regulation of canonical NF-kappaB signal transduction / electron transfer activity / periplasmic space / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / iron ion binding / G protein-coupled receptor signaling pathway / phosphorylation / dendrite / synapse / positive regulation of cell population proliferation / heme binding / negative regulation of apoptotic process / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
5-Hydroxytryptamine 2B 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 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Soluble cytochrome b562 / 5-hydroxytryptamine receptor 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsWacker, D. / Wang, S. / McCorvy, J.D. / Betz, R.M. / Venkatakrishnan, A.J. / Levit, A. / Lansu, K. / Schools, Z.L. / Che, T. / Nichols, D.E. ...Wacker, D. / Wang, S. / McCorvy, J.D. / Betz, R.M. / Venkatakrishnan, A.J. / Levit, A. / Lansu, K. / Schools, Z.L. / Che, T. / Nichols, D.E. / Shoichet, B.K. / Dror, R.O. / Roth, B.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)Psychoactive Drug Screening Program (PDSP) United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)U19MH82441 United States
CitationJournal: Cell / Year: 2017
Title: Crystal Structure of an LSD-Bound Human Serotonin Receptor.
Authors: Wacker, D. / Wang, S. / McCorvy, J.D. / Betz, R.M. / Venkatakrishnan, A.J. / Levit, A. / Lansu, K. / Schools, Z.L. / Che, T. / Nichols, D.E. / Shoichet, B.K. / Dror, R.O. / Roth, B.L.
History
DepositionNov 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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 1.6Oct 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

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5016
Polymers45,2331
Non-polymers1,2685
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.195, 119.177, 170.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562 / / 5-HT2B / Serotonin receptor 2B / Cytochrome b-562 / 5-HT2B / Serotonin receptor 2B


Mass: 45233.012 Da / Num. of mol.: 1 / Mutation: M144W, M1007W, H1102I, R1106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: HTR2B, cybC / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P41595, UniProt: P0ABE7

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Non-polymers , 6 types, 6 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.: 1 / Source method: obtained synthetically / Formula: C20H25N3O
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: 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
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Tris/HCl pH 7.5-8.0, 90-130 mM potassium phosphate monobasic, 28-30% PEG400
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 12422 / % possible obs: 90.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 63.91 Å2 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.087 / Rrim(I) all: 0.174 / Χ2: 1.63 / Net I/av σ(I): 9.442 / Net I/σ(I): 8.1 / Num. measured all: 42654
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.9-33.40.7830.563192.2
3-3.123.40.6590.687191.9
3.12-3.273.40.4990.778192
3.27-3.443.40.3540.866191.8
3.44-3.653.50.2630.924192.1
3.65-3.933.40.1730.962191.6
3.93-4.333.40.1270.975190.8
4.33-4.953.40.1120.979190.5
4.95-6.233.40.0990.987188.7
6.23-303.40.0770.99183.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IB4

4ib4


Resolution: 2.9→29.164 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.04
RfactorNum. reflection% reflection
Rfree0.2628 638 5.15 %
Rwork0.2098 --
obs0.2125 12393 89.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 185.12 Å2 / Biso mean: 62.4857 Å2 / Biso min: 26.15 Å2
Refinement stepCycle: final / Resolution: 2.9→29.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 83 1 3023
Biso mean--64.22 53.17 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033092
X-RAY DIFFRACTIONf_angle_d0.8484231
X-RAY DIFFRACTIONf_chiral_restr0.029524
X-RAY DIFFRACTIONf_plane_restr0.004512
X-RAY DIFFRACTIONf_dihedral_angle_d11.6451081
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9002-3.12380.3151240.25732279240389
3.1238-3.43780.29031300.25642356248692
3.4378-3.93420.27951240.21592411253592
3.9342-4.95270.20581210.19012373249491
4.9527-29.16530.27471390.19392336247586
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0198-0.03230.14022.15550.47070.42670.0452-0.06820.03490.1524-0.0913-0.21050.09270.04670.05210.46150.03750.01440.33470.02790.2148-21.9482-15.7463-0.4471
24.27131.0007-1.05537.5586-1.03274.5493-0.0443-0.04480.0417-0.62310.02480.2392-0.19610.1457-0.10130.4981-0.0942-0.05180.64320.06170.246-43.929-6.1836-43.8908
33.5155-0.32061.01121.19220.54332.12890.24440.06150.03870.2207-0.0962-0.00530.47660.1282-0.12820.7251-0.0381-0.03160.30910.08960.3194-27.5307-22.9025-5.2819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 248 )A41 - 248
2X-RAY DIFFRACTION2chain 'A' and (resid 1001 through 1106 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 313 through 400 )A313 - 400

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