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- PDB-1r1k: Crystal structure of the ligand-binding domains of the heterodime... -

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Basic information

Entry
Database: PDB / ID: 1r1k
TitleCrystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to ponasterone A
Components
  • Ecdysone receptor
  • ULTRASPIRACLE PROTEIN
Keywordshormone/growth factor receptor / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / HETERODIMER / ALPHA-HELICAL SANDWICH / Structural Proteomics in Europe / SPINE / Structural Genomics / hormone-growth factor receptor COMPLEX
Function / homology
Function and homology information


ecdysone binding / ecdysone receptor signaling pathway / nuclear steroid receptor activity / RNA polymerase II transcription regulator complex / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding ...ecdysone binding / ecdysone receptor signaling pathway / nuclear steroid receptor activity / RNA polymerase II transcription regulator complex / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / 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 ...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 / Double treble clef zinc finger, C4 type / 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
Chem-EPH / 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE / Ecdysone receptor / Gene regulation protein
Similarity search - Component
Biological speciesHeliothis virescens (tobacco budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBillas, I.M.L. / Iwema, T. / Garnier, J.-M. / Mitschler, A. / Rochel, N. / Moras, D. / Structural Proteomics in Europe (SPINE)
CitationJournal: Nature / Year: 2003
Title: Structural adaptability in the ligand-binding pocket of the ecdysone hormone receptor.
Authors: Billas, I.M.L. / Iwema, T. / Garnier, J.M. / Mitschler, A. / Rochel, N. / Moras, D.
History
DepositionSep 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence no suitable sequence database reference was available for chains A or D, at the time of ...sequence no suitable sequence database reference was available for chains A or D, at the time of processing this file

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Ecdysone receptor
A: ULTRASPIRACLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4954
Polymers60,3212
Non-polymers1,1752
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-18 kcal/mol
Surface area21630 Å2
MethodPISA
2
D: Ecdysone receptor
A: ULTRASPIRACLE PROTEIN
hetero molecules

D: Ecdysone receptor
A: ULTRASPIRACLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9918
Polymers120,6414
Non-polymers2,3494
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area12050 Å2
ΔGint-50 kcal/mol
Surface area41260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.401, 57.401, 302.696
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ecdysone receptor / Ecdysteroid receptor / 20-hydroxy-ecdysone receptor / 20E receptor / HvEcR


Mass: 30368.961 Da / Num. of mol.: 1 / Fragment: hormone binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Gene: ECR OR NR1H1 / Plasmid: pET32b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O18473
#2: Protein ULTRASPIRACLE PROTEIN


Mass: 29951.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Plasmid: pACYC11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIF6
#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-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris1droppH8.0
2100 mM1dropNaCl
3100 mM1dropKCl
44 mMCHAPS1drop
52 %(v/v)glycerol1drop
64-6 mg/mlprotein1drop
730 %PEG40001reservoir
80.2 Mammonium sulfate1reservoir
90.1 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 28, 2002 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 13703 / Num. obs: 13703 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rsym value: 0.052
Reflection shellResolution: 2.9→2.97 Å / Rsym value: 0.38 / % possible all: 97.9
Reflection
*PLUS
Redundancy: 9.5 % / Num. measured all: 129598 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Vitamin D receptor, PDB entry 1DB1

1db1


Resolution: 2.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.304 1388 RANDOM
Rwork0.243 --
all0.243 13689 -
obs0.243 13637 -
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3797 0 82 8 3887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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