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- PDB-1r0n: Crystal Structure of Heterodimeric Ecdsyone receptor DNA binding ... -

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Basic information

Entry
Database: PDB / ID: 1r0n
TitleCrystal Structure of Heterodimeric Ecdsyone receptor DNA binding complex
Components
  • Ecdsyone Response Element
  • Ecdysone Response Element
  • Ecdysone receptor
  • Retinoic acid receptor RXR-alpha
KeywordsTranscription/DNA / Ecdysone receptor / nuclear receptor / DNA binding domain / Ultraspiracle / RXR / Transcription-DNA COMPLEX
Function / homology
Function and homology information


repressor ecdysone receptor complex / ecdysis, chitin-based cuticle / larval wandering behavior / regulation of Malpighian tubule diameter / regulation of neuron remodeling / compound eye photoreceptor fate commitment / larval development / ecdysone receptor holocomplex / activator ecdysone receptor complex / dorsal vessel heart proper cell fate commitment ...repressor ecdysone receptor complex / ecdysis, chitin-based cuticle / larval wandering behavior / regulation of Malpighian tubule diameter / regulation of neuron remodeling / 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 / 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 / positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / peripheral nervous system development / Carnitine metabolism / anatomical structure development / ion binding / cardiac muscle tissue development / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / regulation of cellular respiration / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / dendrite morphogenesis / Signaling by Retinoic Acid / DNA binding domain binding / phagocytosis, engulfment / nuclear steroid receptor activity / neuron remodeling / oogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / germ cell development / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / epidermis development / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / long-term memory / response to retinoic acid / core promoter sequence-specific DNA binding / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / steroid binding / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / response to cocaine / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / regulation of autophagy / transcription coregulator binding / determination of adult lifespan / nuclear receptor binding / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis
Similarity search - Function
Ecdysteroid receptor / Ecdysone receptor, ligand-binding domain / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Ecdysteroid receptor / Ecdysone receptor, ligand-binding domain / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / 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) / Retinoic acid receptor RXR-alpha / Ecdysone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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: Ecdsyone Response Element
D: Ecdysone Response Element
A: Retinoic acid receptor RXR-alpha
B: Ecdysone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1878
Polymers32,9254
Non-polymers2624
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.620, 60.260, 115.000
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 RXR), bound to an ecdysone response element (IR-1)

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Components

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DNA chain , 2 types, 2 molecules CD

#1: DNA chain Ecdsyone 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 Retinoic acid receptor RXR-alpha


Mass: 9375.969 Da / Num. of mol.: 1 / Fragment: Retinoid X Receptor DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P19793
#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, 108 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.: 104 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 282 K / Method: vapor diffusion / pH: 5.6
Details: PEG 3350, Lithium Sulfate, Magnesium Sulfate, DTT, Magnesium Chloride, MES, pH 5.6, VAPOR DIFFUSION, temperature 282K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Lithium Sulfate11
3Magnesium Sulfate11
4DTT11
5Magnesium Chloride11
6MES11
7H2O11
8PEG 335012
9Magnesium Sulfate12
10DTT12
11Magnesium Chloride12
12MES12
13H2O12
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
121
131

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2834, 1.2837, 1.2155
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 26, 2002 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28341
21.28371
31.21551
ReflectionResolution: 2.6→30 Å / Num. all: 12840 / Num. obs: 12403 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 27.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 6.7 / Num. unique all: 110 / Rsym value: 0.224 / % possible all: 86.6
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 11884 / Redundancy: 9.8 % / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
% possible obs: 75.4 % / Mean I/σ(I) obs: 5.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→14.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 683925.45 / Data cutoff high rms absF: 683925.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.292 739 6.7 %RANDOM
Rwork0.233 ---
all0.26 12403 --
obs0.233 10992 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.3423 Å2 / ksol: 0.28339 e/Å3
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1-15.05 Å20 Å20 Å2
2---2.61 Å20 Å2
3----12.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.39 Å
Luzzati d res low-15 Å
Luzzati sigma a0.48 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 729 4 104 2138
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.36
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.439 86 5.9 %
Rwork0.346 1382 -
obs--72.7 %
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: 15 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.36

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