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- PDB-6k1q: Human endothelin receptor type-B in complex with inverse agonist ... -

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Basic information

Entry
Database: PDB / ID: 6k1q
TitleHuman endothelin receptor type-B in complex with inverse agonist IRL2500
ComponentsEndothelin B receptor,Endolysin,Endothelin B receptor
KeywordsSIGNALING PROTEIN / alpha helical
Function / homology
Function and homology information


enteric smooth muscle cell differentiation / response to endothelin / endothelin receptor activity / negative regulation of neuron maturation / aldosterone metabolic process / chordate pharynx development / vein smooth muscle contraction / regulation of fever generation / heparin metabolic process / positive regulation of penile erection ...enteric smooth muscle cell differentiation / response to endothelin / endothelin receptor activity / negative regulation of neuron maturation / aldosterone metabolic process / chordate pharynx development / vein smooth muscle contraction / regulation of fever generation / heparin metabolic process / positive regulation of penile erection / neuroblast migration / posterior midgut development / epithelial fluid transport / endothelin receptor signaling pathway / developmental pigmentation / podocyte differentiation / renal sodium ion absorption / protein transmembrane transport / response to sodium phosphate / enteric nervous system development / renal sodium excretion / renin secretion into blood stream / melanocyte differentiation / renal albumin absorption / positive regulation of urine volume / regulation of pH / negative regulation of adenylate cyclase activity / peripheral nervous system development / vasoconstriction / regulation of epithelial cell proliferation / type 1 angiotensin receptor binding / establishment of endothelial barrier / neural crest cell migration / negative regulation of protein metabolic process / response to pain / cGMP-mediated signaling / macrophage chemotaxis / peptide hormone binding / canonical Wnt signaling pathway / viral release from host cell by cytolysis / regulation of heart rate / peptidoglycan catabolic process / Peptide ligand-binding receptors / calcium-mediated signaling / calcium ion transmembrane transport / response to organic cyclic compound / vasodilation / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / nervous system development / gene expression / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / cellular response to lipopolysaccharide / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / host cell cytoplasm / cell surface receptor signaling pathway / defense response to bacterium / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Endothelin receptor B / Endothelin receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Endothelin receptor B / Endothelin receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-D2U / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Endolysin / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNagiri, C. / Shihoya, W. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H06294 Japan
CitationJournal: Commun Biol / Year: 2019
Title: Crystal structure of human endothelin ETBreceptor in complex with peptide inverse agonist IRL2500.
Authors: Nagiri, C. / Shihoya, W. / Inoue, A. / Kadji, F.M.N. / Aoki, J. / Nureki, O.
History
DepositionMay 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothelin B receptor,Endolysin,Endothelin B receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,93414
Polymers52,1281
Non-polymers3,80613
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-8 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.910, 109.910, 291.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Endothelin B receptor,Endolysin,Endothelin B receptor / ET-BR / Endothelin receptor non-selective type / Lysis protein / Lysozyme / Muramidase / ET-BR / ...ET-BR / Endothelin receptor non-selective type / Lysis protein / Lysozyme / Muramidase / ET-BR / Endothelin receptor non-selective type


Mass: 52128.090 Da / Num. of mol.: 1
Mutation: R124Y, K270A,C97A, I137R,S342A, I381A, C396A, C400A, C405A,R124Y, K270A,C97A, I137R,S342A, I381A, C396A, C400A, C405A,R124Y, K270A,C97A, I137R,S342A, I381A, C396A, C400A, C405A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: EDNRB, ETRB / Plasmid: modified pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24530, UniProt: P00720, lysozyme
#2: Chemical ChemComp-D2U / (2~{S})-2-[[(2~{R})-2-[(3,5-dimethylphenyl)carbonyl-methyl-amino]-3-(4-phenylphenyl)propanoyl]amino]-3-(1~{H}-indol-3-yl)propanoic acid


Mass: 573.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H35N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 4.22 Å3/Da / Density % sol: 70.88 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: 30% PEG300, 150 mM NaH2PO4,10 mM TCEP, 100 mM Bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.469 Å / Num. obs: 28018 / % possible obs: 99.9 % / Redundancy: 19.281 % / Biso Wilson estimate: 70.136 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.322 / Rrim(I) all: 0.331 / Χ2: 1.344 / Net I/σ(I): 9.67 / Num. measured all: 540205 / Scaling rejects: 193
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.7619.5155.8350.7488268452645230.7045.98999.9
2.76-2.9519.4432.5891.4380785415541550.852.658100
2.95-3.1818.5621.5242.2570740381238110.9011.567100
3.18-3.4919.1160.7674.4370653369636960.9650.788100
3.49-3.919.680.3639.3164510327832780.9880.372100
3.9-4.519.7820.18518.2757329289828980.9940.19100
4.5-5.5219.3770.13223.9549141253725360.9950.135100
5.52-7.818.8380.12724.9137016196519650.9960.131100
7.8-48.46918.8260.08237.6521763117511560.9960.08598.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.469 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 1251 5 %
Rwork0.2216 23757 -
obs0.2238 25008 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.24 Å2 / Biso mean: 83.7693 Å2 / Biso min: 28.51 Å2
Refinement stepCycle: final / Resolution: 2.7→48.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 249 34 3541
Biso mean--91.49 61.73 -
Num. residues----410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.80820.35261360.32552582271899
2.8082-2.9360.33881360.28932576271299
2.936-3.09080.32941360.264925792715100
3.0908-3.28440.29681380.241426192757100
3.2844-3.53790.2981380.234926232761100
3.5379-3.89380.25331390.196426202759100
3.8938-4.45690.21291390.193726532792100
4.4569-5.61380.22291420.202226812823100
5.6138-48.47720.28341470.222428242971100
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)
12.515-0.90080.10774.0288-1.10183.4160.0327-0.15040.0281-0.0979-0.2618-0.0870.26470.01120.19980.3813-0.12360.01440.3953-0.03080.515139.815541.924931.9392
22.8307-0.9311.09091.3356-0.12380.64220.1414-0.3404-0.2632-0.06560.12380.16930.6095-0.1026-0.11560.4155-0.06170.0670.34160.00570.435548.978132.207728.7928
30.9463-0.4818-0.51020.567-0.18612.2105-0.0592-0.2566-0.2530.0421-0.24310.12560.72120.17860.28170.8711-0.2188-0.00230.5713-0.00310.59138.821925.925331.2921
43.44861.51032.55685.27761.24425.5651-0.0415-0.8565-0.2758-0.1089-0.60470.65050.5911-0.84760.53420.9038-0.16030.09480.99140.090.809919.443914.033665.1505
52.7217-0.10110.32883.2779-1.7072.07410.0447-0.5075-0.01170.4138-0.33920.02170.5613-0.21290.30050.6211-0.16920.0680.54640.01410.611732.444929.982239.2598
65.4209-0.47171.88724.482-1.15566.56430.02040.4498-0.5152-0.3560.40260.44740.1249-0.2072-0.50820.435-0.12510.09260.54690.00060.687128.9338.566331.376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 91 through 203 )A91 - 203
2X-RAY DIFFRACTION2chain 'A' and (resid 204 through 247 )A204 - 247
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 312 )A248 - 312
4X-RAY DIFFRACTION4chain 'A' and (resid 313 through 403 )A313 - 403

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