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- PDB-1r0o: Crystal Structure of the Heterodimeric Ecdysone Receptor DNA-bind... -

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Basic information

Entry
Database: PDB / ID: 1r0o
TitleCrystal Structure of the Heterodimeric Ecdysone Receptor DNA-binding Complex
Components
  • (Ecdysone Response ...) x 2
  • Ecdysone receptor
  • Ultraspiracle proteinEcdysone receptor
KeywordsTranscription/DNA / Ecdsyone receptor / Ultraspiracle / Nuclear receptor / DNA binding domain / Transcription-DNA COMPLEX
Function / homology
Function and homology information


ecdysone biosynthetic process / repressor ecdysone receptor complex / ecdysis, chitin-based cuticle / larval wandering behavior / regulation of Malpighian tubule diameter / cellular response to ecdysone / regulation of neuron remodeling / Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional regulation of white adipocyte differentiation / Regulation of lipid metabolism by PPARalpha ...ecdysone biosynthetic process / repressor ecdysone receptor complex / ecdysis, chitin-based cuticle / larval wandering behavior / regulation of Malpighian tubule diameter / cellular response to ecdysone / regulation of neuron remodeling / Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional regulation of white adipocyte differentiation / Regulation of lipid metabolism by PPARalpha / Signaling by Retinoic Acid / Transcriptional regulation of granulopoiesis / Cytoprotection by HMOX1 / compound eye photoreceptor fate commitment / larval development / ecdysone receptor holocomplex / activator ecdysone receptor complex / dorsal vessel heart proper cell fate commitment / hatching / regulation of hemocyte proliferation / Recycling of bile acids and salts / Carnitine metabolism / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / histoblast morphogenesis / chitin-based cuticle development / SUMOylation of intracellular receptors / chitin-based embryonic cuticle biosynthetic process / Nuclear Receptor transcription pathway / response to ecdysone / Malpighian tubule morphogenesis / larval central nervous system remodeling / VLDLR internalisation and degradation / head involution / ecdysone binding / germ-band shortening / pupariation / ecdysone receptor-mediated signaling pathway / cardioblast differentiation / regulation of development, heterochronic / positive regulation of neuron remodeling / mushroom body development / metamorphosis / border follicle cell migration / : / sperm individualization / imaginal disc-derived wing morphogenesis / positive regulation of circadian sleep/wake cycle, sleep / polytene chromosome / hormone binding / peripheral nervous system development / regulation of organ growth / anatomical structure development / cardiac muscle tissue development / regulation of cellular respiration / dendrite morphogenesis / nuclear steroid receptor activity / neuron remodeling / oogenesis / phagocytosis, engulfment / response to starvation / germ cell development / negative regulation of cell differentiation / long-term memory / epidermis development / core promoter sequence-specific DNA binding / steroid binding / cholesterol homeostasis / transcription corepressor binding / response to cocaine / regulation of autophagy / determination of adult lifespan / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coactivator binding / autophagy / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell adhesion / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / negative regulation of gene expression / signaling receptor binding / negative regulation of DNA-templated transcription / dendrite / lipid binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ecdysteroid receptor / Ecdysone receptor, ligand-binding domain / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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. ...Ecdysteroid receptor / Ecdysone receptor, ligand-binding domain / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein ultraspiracle / Ecdysone receptor
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsDevarakonda, S. / Harp, J.M. / Kim, Y. / Ozyhar, A. / Rastinejad, F.
CitationJournal: Embo J. / Year: 2003
Title: Structure of the Heterodimeric Ecdysone Receptor DNA-binding Complex
Authors: Devarakonda, S. / Harp, J.M. / Kim, Y. / Ozyhar, A. / Rastinejad, F.
History
DepositionSep 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ecdysone Response Element
D: Ecdysone Response Element
A: Ultraspiracle protein
B: Ecdysone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9048
Polymers33,6434
Non-polymers2624
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.370, 59.880, 113.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the macromolecular complex in the asymmetric unit and consists of two DNA binding domains (EcR and USP), bound to an ecdysone response element (IR-1)

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Components

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Ecdysone Response ... , 2 types, 2 molecules CD

#1: DNA chain Ecdysone Response Element


Mass: 5501.567 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain Ecdysone Response Element


Mass: 5492.553 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 2 types, 2 molecules AB

#3: Protein Ultraspiracle protein / Ecdysone receptor / XR2C / Chorion factor 1


Mass: 10093.663 Da / Num. of mol.: 1 / Fragment: Ultraspiracle DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: USP / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P20153
#4: Protein Ecdysone receptor / / Ecdysteroid receptor / 20-hydroxy-ecdysone receptor / 20E receptor


Mass: 12554.819 Da / Num. of mol.: 1 / Fragment: Ecdsyone Receptor DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ECR / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P34021

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Non-polymers , 2 types, 283 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 282 K / Method: vapor diffusion / pH: 5.6
Details: PEG 3350, Sodium Chloride, DTT, Magnesium Chloride, MES, pH 5.6, VAPOR DIFFUSION, temperature 282K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Sodium Chloride11
3DTT11
4Magnesium Chloride11
5MES11
6H2O11
7PEG 335012
8DTT12
9Magnesium Chloride12
10MES12
11H2O12
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Zhao, Q., (2000) J.Mol.Biol., 296, 509.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMTris1drop
20.9 mMprotein1drop
30.45 mMDNA1drop
418-23 %PEG33501reservoir
525 mMTris1reservoir
65 mM1reservoirMgCl2
7400 mM1reservoirNH4Cl
81
91
101
111

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.2834 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2002 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2834 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. all: 17165 / Num. obs: 17114 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 22
Reflection shellResolution: 2.24→2.34 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1540 / Rsym value: 0.456 / % possible all: 97.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 15928 / % possible obs: 99.6 %
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R0N

1r0n


Resolution: 2.24→24.77 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 945327.47 / Data cutoff high rms absF: 945327.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1182 6.9 %RANDOM
Rwork0.232 ---
all0.246 17165 --
obs0.232 17114 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9446 Å2 / ksol: 0.346294 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.24→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 737 4 279 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 2.24→2.38 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 188 6.7 %
Rwork0.359 2602 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.33

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