+
Open data
-
Basic information
Entry | Database: PDB / ID: 4udb | ||||||
---|---|---|---|---|---|---|---|
Title | MR in complex with desisobutyrylciclesonide | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / NUCLEAR HORMONE RECEPTOR / LIGAND COMPLEX / PEPTIDE COMPLEX | ||||||
Function / homology | ![]() labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / cellular response to Thyroglobulin triiodothyronine / estrous cycle ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / TBP-class protein binding / steroid binding / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / hippocampus development / nuclear estrogen receptor binding / nuclear receptor 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 / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / receptor complex / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / DNA-binding transcription factor activity / chromatin binding / chromatin / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Edman, K. / Hogner, A. / Hussein, A. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / JellesmarkJensen, T. / Cavallin, A. / Nilsson, E. ...Edman, K. / Hogner, A. / Hussein, A. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / JellesmarkJensen, T. / Cavallin, A. / Nilsson, E. / Lepisto, M. / Guallar, V. | ||||||
![]() | ![]() Title: Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints. Authors: Edman, K. / Hosseini, A. / Bjursell, M.K. / Aagaard, A. / Wissler, L. / Gunnarsson, A. / Kaminski, T. / Kohler, C. / Backstrom, S. / Jensen, T.J. / Cavallin, A. / Karlsson, U. / Nilsson, E. ...Authors: Edman, K. / Hosseini, A. / Bjursell, M.K. / Aagaard, A. / Wissler, L. / Gunnarsson, A. / Kaminski, T. / Kohler, C. / Backstrom, S. / Jensen, T.J. / Cavallin, A. / Karlsson, U. / Nilsson, E. / Lecina, D. / Takahashi, R. / Grebner, C. / Geschwindner, S. / Lepisto, M. / Hogner, A.C. / Guallar, V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 71 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 823.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 823.2 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4udaC ![]() 4udcC ![]() 4uddC ![]() 2aa2S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 31739.393 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 735-984 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1725.958 Da / Num. of mol.: 1 / Fragment: RESIDUES 1427-1441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 64 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CV7.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CV7.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-DMS / |
---|---|
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-SO4 / |
#6: Chemical | ChemComp-CV7 / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % / Description: NONE |
---|---|
Crystal grow | pH: 8.5 Details: 18% PEG4K, 0.14M LISO4, 85MM TRIS PH 8.5, 15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→50 Å / Num. obs: 14723 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Biso Wilson estimate: 52.01 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.36→2.44 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2AA2 Resolution: 2.36→48.79 Å / Cor.coef. Fo:Fc: 0.9494 / Cor.coef. Fo:Fc free: 0.9399 / SU R Cruickshank DPI: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.28 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.2 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.244 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→48.79 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.36→2.55 Å / Total num. of bins used: 7
|