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- PDB-6dry: Structural Determinants of Activation and Biased Agonism at the 5... -

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Basic information

Entry
Database: PDB / ID: 6dry
TitleStructural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
Components5HT2B receptor, BRIL chimera5-HT2B receptor
KeywordsMEMBRANE PROTEIN / GPCR / 5HT2B / Setotonin receptor / Methylergonovine
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
CHOLESTEROL / Chem-H8D / OLEIC ACID / (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 / Resolution: 2.918 Å
AuthorsMcCorvy, J.D. / Wacker, D. / Wang, S. / Agegnehu, B. / Liu, J. / Lansu, K. / Tribo, A.R. / Olsen, R.H.J. / Che, T. / Jin, J. / Roth, B.L.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)RO1MH61887 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)U19MH82441 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01NS100930 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural determinants of 5-HT2Breceptor activation and biased agonism.
Authors: McCorvy, J.D. / Wacker, D. / Wang, S. / Agegnehu, B. / Liu, J. / Lansu, K. / Tribo, A.R. / Olsen, R.H.J. / Che, T. / Jin, J. / Roth, B.L.
History
DepositionJun 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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: 5HT2B receptor, BRIL chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8108
Polymers46,1491
Non-polymers1,6617
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.662, 119.452, 171.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 5HT2B receptor, BRIL chimera / 5-HT2B receptor / 5-HT2B / Serotonin receptor 2B / Cytochrome b-562


Mass: 46149.016 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: HTR2B, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41595, UniProt: P0ABE7

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Non-polymers , 7 types, 8 molecules

#2: Chemical ChemComp-H8D / (8beta)-N-[(2S)-1-hydroxybutan-2-yl]-6-methyl-9,10-didehydroergoline-8-carboxamide / methylergonovine / Methylergometrine


Mass: 339.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N3O2 / Comment: medication*YM
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: 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
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: 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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Tris/HCl pH 7.2-8.0, 170-190 mM Potassium phosphate monobasic, 30% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 4, 2016
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: 12467 / % possible obs: 91.8 % / Redundancy: 2.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.157 / Net I/σ(I): 7.7
Reflection shellResolution: 2.9→2.99 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 905 / CC1/2: 0.56 / % possible all: 81.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 4IB4

4ib4


Resolution: 2.918→29.681 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33
RfactorNum. reflection% reflection
Rfree0.2717 586 4.71 %
Rwork0.2346 --
obs0.2363 12438 90.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.918→29.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 106 1 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023106
X-RAY DIFFRACTIONf_angle_d0.6264248
X-RAY DIFFRACTIONf_dihedral_angle_d8.571817
X-RAY DIFFRACTIONf_chiral_restr0.036523
X-RAY DIFFRACTIONf_plane_restr0.003512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9175-3.21080.41971360.34222615X-RAY DIFFRACTION82
3.2108-3.67470.34521620.27943067X-RAY DIFFRACTION95
3.6747-4.62690.25261330.21463065X-RAY DIFFRACTION94
4.6269-29.6830.2261550.21073105X-RAY DIFFRACTION92
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)
11.95210.1911-0.0831.79720.24560.71820.09390.0104-0.00920.0506-0.1043-0.126-0.16820.09060.110.42360.01220.00680.3385-0.01070.3777-21.7908-16.047-0.0137
23.48332.3914-0.0125.36921.11876.9163-0.37560.26940.2573-0.32320.16560.2995-0.2210.17270.17290.4076-0.0055-0.05810.84430.07490.559-44.2483-6.2518-43.9525
32.43940.41371.23281.82520.88651.63560.2387-0.1095-0.06420.3186-0.10180.03780.15550.0822-0.05540.68330.02810.03680.38940.07110.4791-27.5882-23.0559-5.3212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1001 through 1106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 313 through 400 )

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