[English] 日本語
Yorodumi
- PDB-2han: Structural basis of heterodimeric ecdysteroid receptor interactio... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 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 / autophagic cell death / positive regulation of circadian sleep/wake cycle, sleep / polytene chromosome / hormone binding / peripheral nervous system development / regulation of organ growth / regulation of cellular respiration / cardiac muscle tissue development / bile acid signaling pathway / dendrite morphogenesis / nuclear steroid receptor activity / neuron remodeling / phagocytosis, engulfment / oogenesis / germ cell development / response to starvation / negative regulation of cell differentiation / epidermis development / long-term memory / core promoter sequence-specific DNA binding / steroid binding / transcription corepressor binding / response to cocaine / regulation of autophagy / cholesterol homeostasis / determination of adult lifespan / RNA polymerase II transcription regulatory region sequence-specific DNA binding / autophagy / transcription coactivator binding / negative regulation of inflammatory response / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cell differentiation / transcription cis-regulatory region binding / cell adhesion / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / signaling receptor binding / negative regulation of DNA-templated transcription / lipid binding / dendrite / 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more