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

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Basic information

Entry
Database: PDB / ID: 7bjv
TitleCrystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to the synthetic agonist BYI09181
Components
  • Ecdysone Receptor
  • Ultraspiracle proteinEcdysone receptor
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-EPH / DI(HYDROXYETHYL)ETHER / Chem-U0H / Protein ultraspiracle homolog
Similarity search - Component
Biological speciesHeliothis virescens (tobacco budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 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
B: Ultraspiracle protein
C: Ultraspiracle protein
D: Ecdysone Receptor
E: Ecdysone Receptor
F: Ecdysone Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,40116
Polymers180,8156
Non-polymers3,58710
Water1,65792
1
A: Ultraspiracle protein
D: Ecdysone Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3775
Polymers60,2722
Non-polymers1,1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-26 kcal/mol
Surface area21750 Å2
MethodPISA
2
B: Ultraspiracle protein
E: Ecdysone Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4595
Polymers60,2722
Non-polymers1,1873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-14 kcal/mol
Surface area20250 Å2
MethodPISA
3
C: Ultraspiracle protein
F: Ecdysone Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5656
Polymers60,2722
Non-polymers1,2944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-17 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.035, 147.035, 162.306
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11F-602-

PEG

21A-612-

HOH

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein Ultraspiracle protein / Ecdysone receptor


Mass: 29951.760 Da / Num. of mol.: 3
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.: 3 / 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 , 5 types, 102 molecules

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


Mass: 709.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-U0H / ~{N}-~{tert}-butyl-2-methoxy-~{N}'-(3-methoxy-2-methyl-phenyl)carbonyl-pyridine-3-carbohydrazide


Mass: 371.430 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H25N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, and 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.7749 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 3.05→49.79 Å / Num. obs: 37522 / % possible obs: 95.86 % / Redundancy: 7.2 % / Biso Wilson estimate: 60.56 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 27.48
Reflection shellResolution: 3.05→3.159 Å / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 5.49 / Num. unique obs: 3604 / % possible all: 93.97

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R20

1r20


Resolution: 3.05→49.79 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1880 5.01 %
Rwork0.196 35613 -
obs0.1986 37493 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.41 Å2 / Biso mean: 66.7194 Å2 / Biso min: 20.2 Å2
Refinement stepCycle: final / Resolution: 3.05→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11385 0 250 92 11727
Biso mean--69.15 46.14 -
Num. residues----1441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.05-3.130.371120.23332667277994
3.13-3.220.29181430.2222634277794
3.22-3.330.25661200.21282665278594
3.33-3.450.24131740.22594276893
3.45-3.590.25031700.19572632280293
3.59-3.750.26621380.17872653279194
3.75-3.950.25361380.16622654279294
3.95-4.190.23741450.17172703284895
4.19-4.520.21011250.16922771289697
4.52-4.970.22221610.18452839300099
4.97-5.690.24121470.209228783025100
5.69-7.160.28861580.247629023060100
7.17-49.790.2311490.200430213170100
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)
11.2267-0.3571-0.28580.68250.23440.0745-0.3783-0.02740.2797-0.17180.4972-0.50350.21310.1874-0.02110.2337-0.20940.12980.3117-0.02670.286697.045860.322261.6788
22.04620.22240.01940.7180.60620.7236-0.0466-0.14940.0735-0.00140.0688-0.09190.07180.0342-0.00320.1789-0.037-0.01950.3077-0.01590.282688.704364.705158.3174
30.3961-0.4101-0.05650.8924-0.40220.383-0.41-0.31310.19560.54530.27180.3008-0.4866-0.283-0.00450.38570.07130.03390.41570.1180.556847.900540.338758.4053
40.068-0.0004-0.03070.10860.15180.1449-0.31530.4029-0.0730.04370.15950.79520.0558-0.036-0.0030.40570.01480.03930.38030.09130.79437.313126.703555.8641
50.4953-0.48350.07161.2135-0.03960.9542-0.03130.0441-0.3365-0.04260.10860.3488-0.1987-0.117-0.2270.24460.00420.06880.24430.09960.451847.153124.860757.882
60.739-0.6136-0.14670.8237-0.16770.3054-0.060.03920.57590.16530.1149-0.125-0.3877-0.18090.21520.19430.1105-0.12430.27090.04210.952650.660545.665955.4268
70.05660.00850.02850.01070.00410.00770.0908-0.27540.08240.8263-0.33180.06050.72740.1624-00.5949-0.04870.07840.4449-0.06190.425793.64913.591276.9159
80.90960.2138-0.13870.0957-0.32881.74340.06230.2898-0.07660.15640.06310.6099-0.19-0.03881.48990.4313-0.0483-0.03890.1337-0.45270.522585.6350.552853.4268
90.60280.14580.1930.436-0.38670.439-0.0892-0.137-0.3260.01920.07640.2915-0.04760.013400.3932-0.01990.02590.30080.0160.392190.53538.468659.5086
100.00430.0031-0.00290.01140.03240.060.43750.1233-0.0169-0.0027-0.52850.3613-0.00890.4838-0.00030.67-0.0480.02320.7144-0.07350.9404115.48960.429757.9976
110.70760.70880.31480.8674-0.12571.113-0.06980.194-0.2757-0.010.1055-0.5643-0.08790.00230.0120.3014-0.02420.05920.2737-0.05950.4368102.63919.374257.6698
120.3877-0.0175-0.01330.38710.11620.15760.23980.1817-0.32580.0832-0.2540.0586-0.59420.3065-0.01240.4016-0.0578-0.08150.4748-0.04570.2669101.738624.727970.8724
130.3714-0.6488-0.27041.1516-0.01930.9131-0.0171-0.2251-0.1401-0.2489-0.07350.197-0.1421-0.1944-0.02560.25480.0097-0.00270.28920.03410.404191.932611.141456.1331
140.44870.0336-0.09670.6256-0.10710.0374-0.1669-0.01180.5422-0.03180.32030.398-0.0138-0.19760.47140.22240.0954-0.18220.5448-0.10010.72352.764965.852456.2935
150.00890.0081-0.05150.55870.09890.5453-0.05580.1951-0.22710.46630.3044-0.37690.5513-0.14380.23411.3351-0.3385-0.34851.1057-0.19230.696958.382755.782629.3132
160.2315-0.6474-0.12291.73140.44350.43860.105-0.3811-0.2291-0.7087-0.04560.75360.2089-0.68350.02270.4921-0.159-0.16590.65370.11690.461563.779858.216233.7808
170.13310.1606-0.05041.5293-0.7121.1661-0.12190.46320.0967-0.50830.24040.42960.1392-1.05430.12920.3622-0.0971-0.05060.45910.13180.478865.166361.645743.5646
180.6790.01320.43080.0198-0.03560.9474-0.16230.3568-0.1679-0.15410.1210.07490.04420.2373-0.12350.923-0.17330.21280.3582-0.13140.458470.38445.042534.1983
190.13830.05810.27560.24510.24490.8350.21520.1546-0.1644-0.3321-0.1476-0.26650.0890.17810.00210.3659-0.0940.0210.30370.03660.427469.146658.537249.2488
200.0563-0.05110.05630.1445-0.12290.0689-0.1366-0.13440.44280.36370.07980.0777-0.48060.40750.00010.53270.02520.06870.4650.01680.657562.573768.75460.3698
210.3931-0.31130.06740.1197-0.02390.0039-0.15220.3143-0.2203-0.14310.0864-0.08470.363-0.0520.03440.3448-0.10730.00270.43390.01780.329175.2560.681840.9916
221.6409-0.3188-0.69940.08840.27171.55480.28120.1603-0.7944-0.0618-0.4812-0.4825-0.37890.2141-0.29090.665-0.0750.10610.1843-0.09170.707663.9895-0.992956.4953
230.7128-0.06890.70510.97791.00391.89090.35030.5409-0.4383-0.0517-0.06080.01530.2427-0.61670.88470.6046-0.08250.24280.6731-0.38460.190767.270910.48135.2539
240.2954-0.36580.08950.5937-0.4060.5411-0.11720.3339-0.3968-0.37390.14220.29330.31930.1754-0.12720.4234-0.1156-0.01450.5794-0.16940.466561.789111.06344.5867
250.13810.12820.0210.5176-0.18630.1114-0.03590.0047-0.0429-0.08880.02810.05710.3628-0.2650.15561.0745-0.30250.53180.7787-0.13410.70876.37116.868336.7236
260.07380.1432-0.2020.3218-0.44310.5684-0.0950.30550.62830.0224-0.251-0.4604-0.3286-0.0367-0.51080.3033-0.08610.01520.50980.25330.427370.277925.505943.2112
270.4184-0.17390.12670.76930.45710.92680.1687-0.23990.02430.2080.05250.10920.3357-0.34260.00360.223-0.0165-0.03390.21740.0630.503156.37857.945756.8064
280.1886-0.1818-0.45810.22120.41280.9494-0.15940.2959-0.10560.2331-0.12640.0339-0.1816-0.2118-0.66970.3410.046-0.03550.47380.06170.140758.371519.760242.4831
291.31020.0088-0.19090.60650.63460.57780.04470.50160.5458-0.1987-0.1707-0.7385-0.34410.3596-0.31780.4215-0.140.06840.39110.16790.6214109.870738.662344.0877
300.5720.07740.10250.9973-0.07951.49530.06180.02230.1494-0.3049-0.0144-0.2594-0.2180.13370.0050.4769-0.0437-0.0170.27590.01170.3591103.102632.88449.363
311.0663-0.40530.28110.5023-0.59221.12770.10170.01250.0288-0.7230.20020.4223-0.5157-0.3090.34780.6527-0.0958-0.08960.27860.04990.2346100.178325.380643.4518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 205 through 239 )A205 - 239
2X-RAY DIFFRACTION2chain 'A' and (resid 240 through 464 )A240 - 464
3X-RAY DIFFRACTION3chain 'B' and (resid 205 through 285 )B205 - 285
4X-RAY DIFFRACTION4chain 'B' and (resid 286 through 321 )B286 - 321
5X-RAY DIFFRACTION5chain 'B' and (resid 322 through 437 )B322 - 437
6X-RAY DIFFRACTION6chain 'B' and (resid 438 through 463 )B438 - 463
7X-RAY DIFFRACTION7chain 'C' and (resid 204 through 218 )C204 - 218
8X-RAY DIFFRACTION8chain 'C' and (resid 219 through 239 )C219 - 239
9X-RAY DIFFRACTION9chain 'C' and (resid 240 through 299 )C240 - 299
10X-RAY DIFFRACTION10chain 'C' and (resid 300 through 321 )C300 - 321
11X-RAY DIFFRACTION11chain 'C' and (resid 322 through 384 )C322 - 384
12X-RAY DIFFRACTION12chain 'C' and (resid 385 through 412 )C385 - 412
13X-RAY DIFFRACTION13chain 'C' and (resid 413 through 464 )C413 - 464
14X-RAY DIFFRACTION14chain 'D' and (resid 286 through 307 )D286 - 307
15X-RAY DIFFRACTION15chain 'D' and (resid 308 through 333 )D308 - 333
16X-RAY DIFFRACTION16chain 'D' and (resid 334 through 355 )D334 - 355
17X-RAY DIFFRACTION17chain 'D' and (resid 356 through 397 )D356 - 397
18X-RAY DIFFRACTION18chain 'D' and (resid 398 through 413 )D398 - 413
19X-RAY DIFFRACTION19chain 'D' and (resid 414 through 454 )D414 - 454
20X-RAY DIFFRACTION20chain 'D' and (resid 455 through 480 )D455 - 480
21X-RAY DIFFRACTION21chain 'D' and (resid 481 through 532 )D481 - 532
22X-RAY DIFFRACTION22chain 'E' and (resid 287 through 308 )E287 - 308
23X-RAY DIFFRACTION23chain 'E' and (resid 309 through 355 )E309 - 355
24X-RAY DIFFRACTION24chain 'E' and (resid 356 through 397 )E356 - 397
25X-RAY DIFFRACTION25chain 'E' and (resid 398 through 404 )E398 - 404
26X-RAY DIFFRACTION26chain 'E' and (resid 405 through 430 )E405 - 430
27X-RAY DIFFRACTION27chain 'E' and (resid 431 through 480 )E431 - 480
28X-RAY DIFFRACTION28chain 'E' and (resid 481 through 528 )E481 - 528
29X-RAY DIFFRACTION29chain 'F' and (resid 286 through 364 )F286 - 364
30X-RAY DIFFRACTION30chain 'F' and (resid 365 through 480 )F365 - 480
31X-RAY DIFFRACTION31chain 'F' and (resid 481 through 529 )F481 - 529

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