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- PDB-1r20: Crystal structure of the ligand-binding domains of the heterodime... -

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Basic information

Entry
Database: PDB / ID: 1r20
TitleCrystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to the synthetic agonist BYI06830
Components
  • ECDYSONE RECEPTOR
  • ULTRASPIRACLE PROTEIN
Keywordshormone/growth factor receptor / NUCLEAR RECEPTOR / 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 / Chem-HWG / Ecdysone receptor / Gene regulation protein
Similarity search - Component
Biological speciesHeliothis virescens (tobacco budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 25, 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 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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. In chain D the following residues were mutated compared to the wild- type protein: W303Y, A361S, L456S, C483S.

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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)61,2654
Polymers60,1582
Non-polymers1,1062
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-24 kcal/mol
Surface area21130 Å2
MethodPISA
2
A: ULTRASPIRACLE PROTEIN
D: ECDYSONE RECEPTOR
hetero molecules

A: ULTRASPIRACLE PROTEIN
D: ECDYSONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5308
Polymers120,3174
Non-polymers2,2134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area11510 Å2
ΔGint-63 kcal/mol
Surface area40320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.429, 149.429, 61.058
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIF6
#2: Protein ECDYSONE RECEPTOR


Mass: 30206.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: O18473
#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-HWG / N-(TERT-BUTYL)-3,5-DIMETHYL-N'-[(5-METHYL-2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)CARBONYL]BENZOHYDRAZIDE / 3,5-DIMETHYL-BENZOIC ACID N-TERT-BUTYL-N'-(5-METHYL-2,3-DIHYDRO-BENZO[1,4]DIOXINE-6-CARBONYL)-HYDRAZIDE / BYI6830


Mass: 396.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 1000, PEG 8000, MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING 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
710 %PEG10001reservoir
810 %PEG80001reservoir
90.3 M1reservoirMgCl2
100.1 MHEPES1reservoirpH7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9393
SYNCHROTRONESRF ID14-420.9393
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 12, 2002
ADSC QUANTUM 42CCDJun 14, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. all: 15421 / Num. obs: 15421 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.072
Reflection shellResolution: 3→3.07 Å / Rsym value: 0.355 / % possible all: 85.6
Reflection
*PLUS
Highest resolution: 3 Å / Redundancy: 8.3 % / Num. measured all: 127854 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 85.6 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.289 1532 RANDOM
Rwork0.244 --
all0.244 15830 -
obs0.244 15108 -
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3717 0 78 11 3806
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
Refinement
*PLUS
Highest resolution: 3 Å / % 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_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24

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