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- PDB-7bju: Crystal structure of the ligand-binding domains of the heterodime... -

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Basic information

Entry
Database: PDB / ID: 7bju
TitleCrystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to the synthetic agonist BYI08346
Components
  • Ecdysone Receptor
  • Ultraspiracle Protein
KeywordsTRANSCRIPTION / Nuclear Receptor / Ligand-Binding Domain / Ecdysone receptor / dibenzoylhydrazine
Function / homology
Function and homology information


nuclear steroid receptor activity / sequence-specific DNA binding / DNA-binding transcription factor activity / zinc ion binding / nucleus
Similarity search - Function
Retinoid X receptor/HNF4 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor ...Retinoid X receptor/HNF4 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Chem-834 / Chem-EPH / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Protein ultraspiracle homolog
Similarity search - Component
Biological speciesHeliothis virescens (tobacco budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsBrowning, C. / McEwen, A.G. / Billas, I.M.L.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-01 France
CitationJournal: J Pestic Sci / Year: 2021
Title: Nonsteroidal ecdysone receptor agonists use a water channel for binding to the ecdysone receptor complex EcR/USP.
Authors: Browning, C. / McEwen, A.G. / Mori, K. / Yokoi, T. / Moras, D. / Nakagawa, Y. / Billas, I.M.L.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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: Ultraspiracle Protein
D: Ecdysone Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0588
Polymers60,2722
Non-polymers1,7876
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-21 kcal/mol
Surface area21490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.875, 147.875, 59.776
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Ultraspiracle Protein


Mass: 29951.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ligand-Binding Domain / Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Gene: B5V51_5554 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2A4K9Z3
#2: Protein Ecdysone Receptor


Mass: 30319.781 Da / Num. of mol.: 1 / Mutation: W303Y, A316S, L456S, C483S
Source method: isolated from a genetically manipulated source
Details: Ligand-Binding Domain / Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 7 types, 94 molecules

#3: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE


Mass: 709.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-834 / N-[2-(2-chlorophenyl)-4-methyl-5-(1-methylethyl)-1H-imidazol-1-yl]-5-methyl-2,3-dihydro-1,4-benzodioxine-6-carboxamide / N-(2-(2-chlorophenyl)-5-isopropyl-4-methyl-1H-imidazol-1-yl)-5-methyl-2,3-dihyrobenzo[b][1,4]dioxine-6-carboxamide


Mass: 425.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 1000, 10% PEG 8000, 0.3M MgCl2, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.85→48.4 Å / Num. obs: 17798 / % possible obs: 99.92 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 39.8
Reflection shellResolution: 2.85→2.952 Å / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 7 / Num. unique obs: 1738 / % possible all: 99.94

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
AMoREphasing
PHENIXdev 3951refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R20

1r20


Resolution: 2.85→48.4 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 939 5.28 %
Rwork0.1827 16855 -
obs0.1849 17794 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.91 Å2 / Biso mean: 63.7195 Å2 / Biso min: 24.58 Å2
Refinement stepCycle: final / Resolution: 2.85→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 122 88 4020
Biso mean--67.63 52.23 -
Num. residues----479
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.85-30.2831520.228623472499
3-3.190.26331490.219123582507
3.19-3.430.28741460.199923622508
3.43-3.780.20471480.179723802528
3.78-4.330.2011200.151924362556
4.33-5.450.20591030.168924602563
5.45-48.40.22861210.190925122633
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)
12.086-2.67181.46513.389-1.86841.0278-0.1013-0.8762-0.28111.06220.68040.75180.31430.15540.22480.4770.02560.07460.5772-0.06190.3256-9.533560.862650.375
21.023-0.836-0.10451.87641.31521.680.1431-0.3581.0401-0.566-0.08550.5795-0.6935-0.22471.2740.3923-0.1327-0.27680.54960.00040.6789-26.578860.848427.4841
31.8828-0.2156-0.22231.1106-0.98920.61110.008-0.262-0.08020.08730.00730.29210.1036-0.18780.00010.2429-0.0105-0.01310.3811-0.04050.3591-17.298259.81133.6789
42.6032-0.41282.14131.6670.69562.4041-0.4155-0.5163-0.4969-0.684-0.55960.67860.5511-0.3251-0.14490.60260.00240.16830.4018-0.0150.858-12.424435.06430.1697
52.61470.77680.02532.0612-0.21112.55790.0155-0.2013-0.39320.0988-0.017-0.08940.2176-0.0704-00.23160.0121-0.01270.30810.00210.3467-5.914153.724136.3666
62.99431.26060.66111.61870.04930.7977-0.2264-0.09770.1909-0.13570.11830.3494-0.0984-0.254-0.00030.30280.0182-0.02160.3463-0.00630.3716-14.150660.651130.5876
70.89540.61-0.63762.2768-1.60236.0586-0.35770.308-0.2350.2538-0.2833-1.3657-1.571-0.1859-0.66580.4890.21260.06110.67270.0870.848624.697654.828733.1807
80.0064-0.1273-0.02972.0490.56940.1504-0.38520.921-0.7930.73261.2114-1.3206-1.0172-0.2393-0.06291.27620.08420.32731.6515-0.21050.891723.552364.36839.7233
90.7320.53390.32711.0433-0.60441.4903-0.08290.6981-0.2154-0.32390.0351-0.73410.32130.74790.12470.5208-0.0050.17320.7168-0.06870.392212.902656.878214.5818
104.44093.90820.1213.54550.84313.4854-0.4190.57861.2382-1.3908-0.01110.9655-1.8286-0.1606-1.12761.0207-0.2474-0.10210.6530.24090.311310.070375.645413.7574
110.6750.2260.43890.8419-0.96111.7589-0.02530.21270.1038-0.4677-0.12010.0911-0.14930.1715-0.00020.3627-0.012-0.00220.3495-0.05860.41658.465762.116725.0993
121.38070.18040.17770.42130.37281.17540.2609-0.8238-0.91480.7674-0.3067-0.71790.84520.2667-0.280.44710.0113-0.04520.54170.05220.653714.772551.729236.6342
131.7067-0.5-0.93540.93610.11850.502-0.46660.35450.1546-0.1733-0.1126-0.0508-0.40010.0687-0.03820.4737-0.077-0.02450.4641-0.03650.28972.158961.320923.5064
141.60761.5378-0.86451.4717-0.83060.47880.02271.3062-0.6284-1.8565-0.5555-0.0197-0.01220.6931-0.09921.17550.2038-0.00270.8963-0.10260.4954.577956.664.4779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 205 through 218 )A205 - 218
2X-RAY DIFFRACTION2chain 'A' and (resid 219 through 239 )A219 - 239
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 301 )A240 - 301
4X-RAY DIFFRACTION4chain 'A' and (resid 302 through 321 )A302 - 321
5X-RAY DIFFRACTION5chain 'A' and (resid 322 through 412 )A322 - 412
6X-RAY DIFFRACTION6chain 'A' and (resid 413 through 464 )A413 - 464
7X-RAY DIFFRACTION7chain 'D' and (resid 286 through 307 )D286 - 307
8X-RAY DIFFRACTION8chain 'D' and (resid 308 through 319 )D308 - 319
9X-RAY DIFFRACTION9chain 'D' and (resid 332 through 387 )D332 - 387
10X-RAY DIFFRACTION10chain 'D' and (resid 388 through 413 )D388 - 413
11X-RAY DIFFRACTION11chain 'D' and (resid 414 through 454 )D414 - 454
12X-RAY DIFFRACTION12chain 'D' and (resid 455 through 480 )D455 - 480
13X-RAY DIFFRACTION13chain 'D' and (resid 481 through 514 )D481 - 514
14X-RAY DIFFRACTION14chain 'D' and (resid 515 through 528 )D515 - 528

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