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- PDB-4ozt: crystal structure of the ligand binding domains of the Bovicola o... -

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Basic information

Entry
Database: PDB / ID: 4ozt
Titlecrystal structure of the ligand binding domains of the Bovicola ovis ecdysone receptor EcR/USP heterodimer (PonA crystal)
Components
  • Ecdysone receptor
  • Retinoid X receptor
KeywordsTRANSCRIPTION / ecdysone receptor / USP / PonA
Function / homology
Function and homology information


ecdysone binding / ecdysone receptor signaling pathway / nuclear steroid receptor activity / nuclear receptor activity / sequence-specific DNA binding / DNA-binding transcription factor activity / zinc ion binding / nucleus
Similarity search - Function
Ecdysteroid receptor / Ecdysone receptor, ligand-binding domain / Retinoid X receptor/HNF4 / Retinoid X Receptor / Retinoid X Receptor / 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. ...Ecdysteroid receptor / Ecdysone receptor, ligand-binding domain / Retinoid X receptor/HNF4 / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
N-ETHYLMALEIMIDE / 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE / Retinoid X receptor, putative / Ecdysone receptor
Similarity search - Component
Biological speciesPediculus humanus subsp. corporis (human body louse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRen, B. / Peat, T.S. / Streltsov, V.A. / Pollard, M. / Fernley, R. / Grusovin, J. / Seabrook, S. / Pilling, P. / Phan, T. / Lu, L. ...Ren, B. / Peat, T.S. / Streltsov, V.A. / Pollard, M. / Fernley, R. / Grusovin, J. / Seabrook, S. / Pilling, P. / Phan, T. / Lu, L. / Lovrecz, G.O. / Graham, L.D. / Hill, R.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Unprecedented conformational flexibility revealed in the ligand-binding domains of the Bovicola ovis ecdysone receptor (EcR) and ultraspiracle (USP) subunits.
Authors: Ren, B. / Peat, T.S. / Streltsov, V.A. / Pollard, M. / Fernley, R. / Grusovin, J. / Seabrook, S. / Pilling, P. / Phan, T. / Lu, L. / Lovrecz, G.O. / Graham, L.D. / Hill, R.J.
History
DepositionFeb 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Ecdysone receptor
U: Retinoid X receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0504
Polymers49,4602
Non-polymers5902
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint2 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.000, 134.000, 95.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ecdysone receptor


Mass: 27482.625 Da / Num. of mol.: 1 / Fragment: UNP residues 281-518
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediculus humanus subsp. corporis (human body louse)
Gene: Phum_PHUM467460 / Production host: Escherichia coli (E. coli) / References: UniProt: E0VVT4
#2: Protein Retinoid X receptor


Mass: 21977.549 Da / Num. of mol.: 1 / Fragment: UNP residues 222-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediculus humanus subsp. corporis (human body louse)
Gene: Phum_PHUM164330 / Production host: Escherichia coli (E. coli) / References: UniProt: E0VFQ5
#3: Chemical ChemComp-P1A / 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE / PONASTERONE A / 25-DEOXYECDYSTERONE / 25-DEOXY-20-HYDROXYECDYSONE,


Mass: 464.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O6
#4: Chemical ChemComp-NEQ / N-ETHYLMALEIMIDE


Mass: 125.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350 with either 0.2 M potassium acetate or 0.2 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9536 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.7→38.8 Å / Num. obs: 24458 / % possible obs: 100 % / Redundancy: 12.1 % / Net I/σ(I): 14.8

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→38.83 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1243 5.1 %
Rwork0.182 --
obs0.184 24355 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 42 61 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053630
X-RAY DIFFRACTIONf_angle_d1.4184925
X-RAY DIFFRACTIONf_dihedral_angle_d14.6231377
X-RAY DIFFRACTIONf_chiral_restr0.179563
X-RAY DIFFRACTIONf_plane_restr0.004630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.80820.35781570.29732492X-RAY DIFFRACTION100
2.8082-2.93590.30941150.25312547X-RAY DIFFRACTION100
2.9359-3.09070.29971390.23792523X-RAY DIFFRACTION100
3.0907-3.28420.27281470.24642536X-RAY DIFFRACTION100
3.2842-3.53760.25411280.19912549X-RAY DIFFRACTION100
3.5376-3.89330.20021410.17022543X-RAY DIFFRACTION100
3.8933-4.4560.18761440.14832573X-RAY DIFFRACTION100
4.456-5.61140.18121350.14872618X-RAY DIFFRACTION100
5.6114-38.83510.17551370.16392731X-RAY DIFFRACTION99
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)
11.2613-0.45091.04262.4759-0.09762.0818-0.2691-0.02210.6817-0.09370.1424-0.6754-0.60920.54050.00140.4106-0.0595-0.06910.29230.01210.485722.04-38.291820.6848
22.49340.8711.31611.34350.85675.12760.30960.4222-0.5911-0.5003-0.1398-0.29640.78130.1776-0.21840.63610.1816-0.09750.5145-0.17560.627918.1498-66.36995.0283
33.09380.00170.55863.50020.57342.57370.03010.27420.1719-0.1385-0.0832-0.0372-0.1093-0.01430.04580.19450.04650.00780.2994-0.01220.245810.2458-47.89169.8657
44.08420.26671.72891.93120.78632.9069-0.1190.71210.8239-0.2941-0.11130.2154-0.11140.29680.22210.36180.10080.01250.37250.01950.46357.0972-36.5297.2752
53.1313.07433.54523.29162.5175.10890.1135-0.20160.48260.7083-0.49810.7462-0.1156-0.398-0.20730.46840.0045-0.00510.5084-0.04480.4248-1.7633-61.61595.0243
64.4250.5705-0.24462.4224-0.2411.80950.1329-0.13760.69010.1529-0.02150.0432-0.3891-0.2835-0.16540.340.12150.01670.39590.05260.5736-18.644-26.26852.5388
73.1008-0.764-0.14882.4937-0.05732.5303-0.0527-0.38860.22930.5080.11960.32890.0526-0.1988-0.11670.41470.07460.09390.3379-0.03820.4088-16.8253-34.529611.7624
83.9320.57830.99593.0048-0.25664.9947-0.0681-0.08740.94110.3622-0.0239-0.459-0.61820.33160.04430.41870.0512-0.04250.2536-0.05050.6147-1.2913-25.71268.2397
94.82890.59662.10471.4199-0.37012.4255-0.118-0.06890.56660.1319-0.06220.0007-0.1189-0.10470.12810.38920.12810.01110.284-0.08430.4192-11.2717-32.73035.6022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'E' AND (RESID 281 THROUGH 301 )
2X-RAY DIFFRACTION2CHAIN 'E' AND (RESID 302 THROUGH 322 )
3X-RAY DIFFRACTION3CHAIN 'E' AND (RESID 323 THROUGH 468 )
4X-RAY DIFFRACTION4CHAIN 'E' AND (RESID 469 THROUGH 495 )
5X-RAY DIFFRACTION5CHAIN 'E' AND (RESID 496 THROUGH 518 )
6X-RAY DIFFRACTION6CHAIN 'U' AND (RESID 196 THROUGH 226 )
7X-RAY DIFFRACTION7CHAIN 'U' AND (RESID 227 THROUGH 285 )
8X-RAY DIFFRACTION8CHAIN 'U' AND (RESID 286 THROUGH 340 )
9X-RAY DIFFRACTION9CHAIN 'U' AND (RESID 341 THROUGH 390 )

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