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- PDB-6iiu: Crystal structure of the human thromboxane A2 receptor bound to r... -

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Basic information

Entry
Database: PDB / ID: 6iiu
TitleCrystal structure of the human thromboxane A2 receptor bound to ramatroban
ComponentsSoluble cytochrome b562,Thromboxane A2 receptor,Rubredoxin,Thromboxane A2 receptor
KeywordsSIGNALING PROTEIN / GPCR / Complex / Antagonist
Function / homology
Function and homology information


thromboxane A2 receptor activity / Prostanoid ligand receptors / alkane catabolic process / positive regulation of smooth muscle contraction / positive regulation of blood pressure / negative regulation of cell migration involved in sprouting angiogenesis / response to testosterone / smooth muscle contraction / positive regulation of blood coagulation / positive regulation of vasoconstriction ...thromboxane A2 receptor activity / Prostanoid ligand receptors / alkane catabolic process / positive regulation of smooth muscle contraction / positive regulation of blood pressure / negative regulation of cell migration involved in sprouting angiogenesis / response to testosterone / smooth muscle contraction / positive regulation of blood coagulation / positive regulation of vasoconstriction / response to nutrient / acrosomal vesicle / guanyl-nucleotide exchange factor activity / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Thromboxane signalling through TP receptor / positive regulation of angiogenesis / G alpha (12/13) signalling events / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / G alpha (q) signalling events / response to ethanol / periplasmic space / electron transfer activity / nuclear speck / inflammatory response / iron ion binding / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / heme binding / plasma membrane
Similarity search - Function
Thromboxane receptor / Prostanoid receptor / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. ...Thromboxane receptor / Prostanoid receptor / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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-A8X / CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Rubredoxin / Soluble cytochrome b562 / Thromboxane A2 receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFan, H. / Zhao, Q. / Wu, B.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDB-SSW-SMC024 China
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Structural basis for ligand recognition of the human thromboxane A2receptor.
Authors: Fan, H. / Chen, S. / Yuan, X. / Han, S. / Zhang, H. / Xia, W. / Xu, Y. / Zhao, Q. / Wu, B.
History
DepositionOct 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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: Soluble cytochrome b562,Thromboxane A2 receptor,Rubredoxin,Thromboxane A2 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9167
Polymers53,2421
Non-polymers1,6746
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-0 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.160, 155.080, 128.130
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 Soluble cytochrome b562,Thromboxane A2 receptor,Rubredoxin,Thromboxane A2 receptor / Cytochrome b-562 / TXA2-R / Prostanoid TP receptor / Rd / TXA2-R / Prostanoid TP receptor


Mass: 53242.238 Da / Num. of mol.: 1 / Mutation: M1007W/H1102I/R1106L/L247A
Source method: isolated from a genetically manipulated source
Details: GPCR protein followed a traditional fusion strategy by introducing a bRIL fusion protein at the N terminus of the receptor and a rubredoxin fusion protein in the third intracellular loop of ...Details: GPCR protein followed a traditional fusion strategy by introducing a bRIL fusion protein at the N terminus of the receptor and a rubredoxin fusion protein in the third intracellular loop of the receptor. The residues from bRIL were numbered with 1001-1106 and the residues from rubredoxin were numbered with 2001 to 2054, with 2001 and 2054 covalently linked to residues 228 and 237 of the receptor, respectively.
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: cybC, TBXA2R / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0ABE7, UniProt: P21731, UniProt: P00268

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Non-polymers , 6 types, 17 molecules

#2: Chemical ChemComp-A8X / 3-[(3R)-3-[(4-fluorophenyl)sulfonylamino]-1,2,3,4-tetrahydrocarbazol-9-yl]propanoic acid / Ramatroban


Mass: 416.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21FN2O4S / Comment: antagonist*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CLR / 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.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.79 Å3/Da / Density % sol: 67.51 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: Magnesium acetate, PEG 500 DME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 27682 / % possible obs: 97.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 66.72 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.3 / % possible all: 89.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PXZ, 1M6T, 1IRO

4pxz

1m6t

1iro


Resolution: 2.5→41.53 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.933 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.247 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1411 5.1 %RANDOM
Rwork0.198 ---
obs0.199 27682 97.6 %-
Displacement parametersBiso mean: 75.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.6937 Å20 Å20 Å2
2--0.7203 Å20 Å2
3----0.0266 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.5→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 96 11 3565
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013637HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094967HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1208SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes552HARMONIC5
X-RAY DIFFRACTIONt_it3637HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion18.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion478SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4258SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.245 121 4.83 %
Rwork0.217 2382 -
all0.218 2503 -
obs--85.52 %
Refinement TLS params.Method: refined / Origin x: 19.8658 Å / Origin y: 160.678 Å / Origin z: 142.328 Å
111213212223313233
T-0.054 Å2-0.0105 Å2-0.0365 Å2--0.264 Å20.0064 Å2---0.177 Å2
L0.8061 °21.4815 °2-0.2299 °2-4.5865 °2-0.866 °2--0.9193 °2
S0.0887 Å °-0.0413 Å °0.0043 Å °0.3724 Å °-0.0915 Å °-0.0857 Å °-0.0846 Å °0.0146 Å °0.0029 Å °
Refinement TLS groupSelection details: { A|* }

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