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- PDB-2han: Structural basis of heterodimeric ecdysteroid receptor interactio... -

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Basic information

Entry
Database: PDB / ID: 2han
TitleStructural basis of heterodimeric ecdysteroid receptor interaction with natural response element hsp27 gene promoter
Components
  • 5'-D(*CP*AP*AP*GP*GP*GP*TP*TP*CP*AP*AP*TP*GP*CP*AP*CP*TP*TP*GP*T)-3'
  • 5'-D(*GP*AP*CP*AP*AP*GP*TP*GP*CP*AP*TP*TP*GP*AP*AP*CP*CP*CP*TP*T)-3'
  • Ecdysone receptor
  • Protein ultraspiracle
KeywordsTranscription/DNA / Transcription regulation / Transcription factor / DNA-binding / Nuclear protein / Nuclear Receptor / Zinc finger / 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 / Transcriptional regulation of white adipocyte differentiation / Regulation of lipid metabolism by PPARalpha / Signaling by Retinoic Acid ...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 / 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 / Recycling of bile acids and salts / Carnitine shuttle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / histoblast morphogenesis / regulation of hemocyte proliferation / chitin-based cuticle development / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / chitin-based embryonic cuticle biosynthetic process / Malpighian tubule morphogenesis / response to ecdysone / larval central nervous system remodeling / VLDLR internalisation and degradation / ecdysone binding / ecdysone receptor signaling pathway / head involution / pupariation / cardioblast differentiation / germ-band shortening / regulation of development, heterochronic / positive regulation of neuron remodeling / mushroom body development / metamorphosis / border follicle cell migration / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / sperm individualization / imaginal disc-derived wing morphogenesis / autophagic cell death / polytene chromosome / positive regulation of circadian sleep/wake cycle, sleep / regulation of cellular respiration / peripheral nervous system development / regulation of organ growth / cardiac muscle tissue development / phagocytosis, engulfment / oogenesis / neuron remodeling / response to starvation / dendrite morphogenesis / germ cell development / hormone binding / nuclear steroid receptor activity / negative regulation of cell differentiation / epidermis development / regulation of macroautophagy / long-term memory / core promoter sequence-specific DNA binding / retinoic acid receptor signaling pathway / intracellular receptor signaling pathway / steroid binding / cholesterol homeostasis / transcription corepressor binding / determination of adult lifespan / response to cocaine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / autophagy / negative regulation of inflammatory response / transcription coactivator binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / cell adhesion / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / signaling receptor binding / negative regulation of gene expression / 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
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 ...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 / 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 / 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: 1.95 Å
AuthorsJakob, M. / Kolodziejczyk, R. / Orlowski, M. / Krzywda, S. / Kowalska, A. / Dutko-Gwozdz, J. / Gwozdz, T. / Kochman, M. / Jaskolski, M. / Ozyhar, A.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Novel DNA-binding element within the C-terminal extension of the nuclear receptor DNA-binding domain.
Authors: Jakob, M. / Kolodziejczyk, R. / Orlowski, M. / Krzywda, S. / Kowalska, A. / Dutko-Gwozdz, J. / Gwozdz, T. / Kochman, M. / Jaskolski, M. / Ozyhar, A.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _diffrn_source.pdbx_synchrotron_site / _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: 5'-D(*CP*AP*AP*GP*GP*GP*TP*TP*CP*AP*AP*TP*GP*CP*AP*CP*TP*TP*GP*T)-3'
D: 5'-D(*GP*AP*CP*AP*AP*GP*TP*GP*CP*AP*TP*TP*GP*AP*AP*CP*CP*CP*TP*T)-3'
A: Protein ultraspiracle
B: Ecdysone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8688
Polymers36,6064
Non-polymers2624
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.716, 59.790, 65.179
Angle α, β, γ (deg.)90.00, 106.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules CD

#1: DNA chain 5'-D(*CP*AP*AP*GP*GP*GP*TP*TP*CP*AP*AP*TP*GP*CP*AP*CP*TP*TP*GP*T)-3'


Mass: 6148.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Natural Ecdysone Response Element
#2: DNA chain 5'-D(*GP*AP*CP*AP*AP*GP*TP*GP*CP*AP*TP*TP*GP*AP*AP*CP*CP*CP*TP*T)-3'


Mass: 6117.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Natural Ecdysone Response Element

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Protein , 2 types, 2 molecules AB

#3: Protein Protein ultraspiracle / XR2C / Chorion factor 1


Mass: 10818.429 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, Cf1, NR2B4 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: P20153
#4: Protein Ecdysone receptor / Ecdysteroid receptor / 20-hydroxy-ecdysone receptor / 20E receptor / EcRH


Mass: 13520.830 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, NR1H1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: P34021

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Non-polymers , 2 types, 226 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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 21% PEG 3350, 0.1 M NaCl, 0.1 M MES, 1 mM DTT, 5 mikroM ZnCl2, 0.1 M LiCl, 10 mM MgCl2 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2NaCl11
3MES11
4DTT11
5ZnCl211
6LiCl11
7MgCl211
8H2O11
9PEG 335012
10NaCl12
11ZnCl212
12LiCl12
13MgCl212
14H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8115 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2004
RadiationMonochromator: triangular horizontal-focusing Si III monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8115 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 25368 / Num. obs: 25368 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1r0o

1r0o


Resolution: 1.95→26.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.242 / SU ML: 0.092 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21706 1272 5.1 %RANDOM
Rwork0.17965 ---
obs0.1816 23899 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.648 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20.23 Å2
2---0.58 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.95→26.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 812 4 222 2386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212226
X-RAY DIFFRACTIONr_bond_other_d0.0020.021577
X-RAY DIFFRACTIONr_angle_refined_deg2.0292.4183149
X-RAY DIFFRACTIONr_angle_other_deg1.11833725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021891
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02315
X-RAY DIFFRACTIONr_nbd_refined0.1880.2382
X-RAY DIFFRACTIONr_nbd_other0.2540.21835
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3610.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0471.5811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.89821290
X-RAY DIFFRACTIONr_scbond_it2.43531415
X-RAY DIFFRACTIONr_scangle_it3.5564.51859
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 84
Rwork0.251 1745

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