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

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Basic information

Entry
Database: PDB / ID: 6drx
TitleStructural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
Components5HT2B receptor, BRIL chimera
KeywordsMEMBRANE PROTEIN / GPCR / 5HT2B / Setotonin receptor / Lisuride
Function / homology
Function and homology information


intestine smooth muscle contraction / 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 / regulation of behavior / phospholipase C-activating serotonin receptor signaling pathway / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity ...intestine smooth muscle contraction / 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 / regulation of behavior / phospholipase C-activating serotonin receptor signaling pathway / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity / embryonic morphogenesis / serotonin receptor signaling pathway / vasoconstriction / neurotransmitter receptor activity / serotonin binding / cardiac muscle hypertrophy / neural crest cell differentiation / neural crest cell migration / : / positive regulation of cell division / G-protein alpha-subunit binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / heart morphogenesis / ERK1 and ERK2 cascade / positive regulation of endothelial cell proliferation / release of sequestered calcium ion into cytosol / GTPase activator activity / positive regulation of cytokine production / calcium-mediated signaling / electron transport chain / intracellular calcium ion homeostasis / G alpha (q) signalling events / chemical synaptic transmission / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / G protein-coupled receptor signaling pathway / iron ion binding / response to xenobiotic stimulus / positive regulation of cell population proliferation / heme binding / synapse / dendrite / negative regulation of apoptotic process / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
5-Hydroxytryptamine 2B receptor / 5-hydroxytryptamine receptor family / Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...5-Hydroxytryptamine 2B receptor / 5-hydroxytryptamine receptor family / Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / Chem-H8G / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 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: 3.1 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
Revision 1.5Nov 6, 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: 5HT2B receptor, BRIL chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1324
Polymers46,0501
Non-polymers1,0823
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.380, 118.550, 168.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 5HT2B receptor, BRIL chimera / 5-HT2B / Serotonin receptor 2B / Cytochrome b-562


Mass: 46049.887 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
#2: Chemical ChemComp-H8G / N,N-diethyl-N'-[(8alpha)-6-methyl-9,10-didehydroergolin-8-yl]urea / lisuride


Mass: 338.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N4O
#3: Chemical ChemComp-CLR / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Tris/HCl pH 7.4-7.7, 30-50 mM Ammonium tartrate dibasic, 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: 3.1→30 Å / Num. obs: 10701 / % possible obs: 97.1 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Net I/σ(I): 10.9
Reflection shellResolution: 3.1→3.17 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 699 / CC1/2: 0.462 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 4IB4

4ib4


Resolution: 3.1→29.257 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.99
RfactorNum. reflection% reflection
Rfree0.2859 495 4.64 %
Rwork0.2434 --
obs0.2453 10675 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 72 1 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022789
X-RAY DIFFRACTIONf_angle_d0.7613833
X-RAY DIFFRACTIONf_dihedral_angle_d9.17901
X-RAY DIFFRACTIONf_chiral_restr0.022486
X-RAY DIFFRACTIONf_plane_restr0.004462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0973-3.40860.34281280.30922361X-RAY DIFFRACTION91
3.4086-3.90080.28331350.25992571X-RAY DIFFRACTION98
3.9008-4.91090.2961050.23562586X-RAY DIFFRACTION97
4.9109-29.25850.26561270.22632662X-RAY DIFFRACTION96
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)
13.1608-0.22460.10712.71380.23640.83150.08580.0559-0.04230.0737-0.0405-0.1358-0.03590.1253-0.01760.60810.0602-0.00590.51930.0610.3824-19.982-14.9377-1.5081
21.06331.2811-0.8095.7112-1.10646.5565-0.0408-0.02970.0599-0.14670.00720.0388-0.1873-0.5697-0.00730.74780.09540.00681.70670.12860.6131-47.197-5.598-45.0425
34.5918-0.0797-0.07343.02930.41594.43990.25650.3544-0.1119-0.1363-0.04830.17510.9927-0.7034-0.21590.7979-0.04540.01420.50070.08850.4454-25.0967-22.8383-5.0947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1001 through 1106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 400 )

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