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- PDB-4ib4: Crystal structure of the chimeric protein of 5-HT2B-BRIL in compl... -

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Basic information

Entry
Database: PDB / ID: 4ib4
TitleCrystal structure of the chimeric protein of 5-HT2B-BRIL in complex with ergotamine
ComponentsChimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562
KeywordsSIGNALING PROTEIN / ELECTRON TRANSPORT / ergotamine / Novel protein engineering / GPCR Network / Membrane protein / PSI-Biology / Structural Genomics / GPCR / GPCR Dock
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 c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) ...5-Hydroxytryptamine 2B receptor / 5-hydroxytryptamine receptor family / Cytochrome c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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 / Ergotamine / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / PALMITIC ACID / 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: 2.7 Å
AuthorsWacker, D. / Wang, C. / Katritch, V. / Han, G.W. / Huang, X. / Vardy, E. / McCorvy, J.D. / Jiang, Y. / Chu, M. / Siu, F.Y. ...Wacker, D. / Wang, C. / Katritch, V. / Han, G.W. / Huang, X. / Vardy, E. / McCorvy, J.D. / Jiang, Y. / Chu, M. / Siu, F.Y. / Liu, W. / Xu, H.E. / Cherezov, V. / Roth, B.L. / Stevens, R.C. / GPCR Network (GPCR)
CitationJournal: Science / Year: 2013
Title: Structural features for functional selectivity at serotonin receptors.
Authors: Wacker, D. / Wang, C. / Katritch, V. / Han, G.W. / Huang, X.P. / Vardy, E. / McCorvy, J.D. / Jiang, Y. / Chu, M. / Siu, F.Y. / Liu, W. / Xu, H.E. / Cherezov, V. / Roth, B.L. / Stevens, R.C.
History
DepositionDec 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3May 15, 2013Group: Database references
Revision 1.4Jun 7, 2017Group: Database references / Structure summary
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)51,71112
Polymers48,2831
Non-polymers3,42811
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.571, 119.750, 170.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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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 /


Mass: 48283.273 Da / Num. of mol.: 1 / Mutation: M144W, M29W, H124I, R128L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: HTR2B, cybC / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P41595, UniProt: P0ABE7

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Non-polymers , 8 types, 20 molecules

#2: Chemical ChemComp-ERM / Ergotamine / Ergotamine


Mass: 581.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35N5O5 / Comment: neurotransmitter, alkaloid*YM
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#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-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 17

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 100 mM Tris/HCl pH 8.0, 100 mM magnesium sulfate and 30% (v/v) PEG400, Lipid Cubic Phase (LCP) , temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 16041 / % possible obs: 90.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 72.1 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.7 / % possible all: 92.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3PBL

3pbl


Resolution: 2.7→24.84 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9267 / SU R Cruickshank DPI: 0.579 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 823 5.2 %RANDOM
Rwork0.2244 ---
obs0.2265 15818 90.69 %-
Displacement parametersBiso mean: 80.04 Å2
Baniso -1Baniso -2Baniso -3
1--2.0121 Å20 Å20 Å2
2---1.2375 Å20 Å2
3---3.2497 Å2
Refine analyzeLuzzati coordinate error obs: 0.429 Å
Refinement stepCycle: LAST / Resolution: 2.7→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 205 9 3063
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONf_bond_d0.0093121HARMONIC2
X-RAY DIFFRACTIONf_angle_deg0.994232HARMONIC2
X-RAY DIFFRACTIONf_dihedral_angle_d1432SINUSOIDAL2
X-RAY DIFFRACTIONf_incorr_chiral_ct
X-RAY DIFFRACTIONf_pseud_angle
X-RAY DIFFRACTIONf_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONf_gen_planes436HARMONIC5
X-RAY DIFFRACTIONf_it3121HARMONIC20
X-RAY DIFFRACTIONf_nbd
X-RAY DIFFRACTIONf_omega_torsion1.91
X-RAY DIFFRACTIONf_other_torsion3.09
X-RAY DIFFRACTIONf_improper_torsion
X-RAY DIFFRACTIONf_chiral_improper_torsion421SEMIHARMONIC5
X-RAY DIFFRACTIONf_sum_occupancies
X-RAY DIFFRACTIONf_utility_distance1HARMONIC1
X-RAY DIFFRACTIONf_utility_angle
X-RAY DIFFRACTIONf_utility_torsion
X-RAY DIFFRACTIONf_ideal_dist_contact3548SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.89 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.254 162 5.59 %
Rwork0.2596 2735 -
all0.2593 2897 -
obs--90.69 %
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)
11.71890.0732-0.47841.52180.61972.7370.09170.01110.1175-0.0336-0.06760.0689-0.0945-0.0891-0.024-0.0480.0189-0.0017-0.2239-0.0207-0.194622.390917.7334-2.6841
22.8264-0.0790.11030.1612-1.39573.27820.0176-0.15090.02920.0616-0.00760.04320.02670.0473-0.01-0.1673-0.073-0.05640.232-0.1484-0.211347.57785.81-45.2388
30.0574-0.50080.14140.00370.099700.00140.01380.0053-0.0019-0.0026-0.00320.0004-0.00140.0012-0.01760.06580.01030.0061-0.0175-0.00155.303633.5433-9.5529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|48 - A|400 }A48 - 400
2X-RAY DIFFRACTION2{ A|1001- A|1106 }A1001 - 1106
3X-RAY DIFFRACTION3{ A|2002 - A|2002 }A2002

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