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- PDB-1xdk: Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain H... -
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Basic information
Entry | Database: PDB / ID: 1xdk | ||||||
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Title | Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex with 9-cis Retinoic Acid and a Fragment of the TRAP220 Coactivator | ||||||
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![]() | HORMONE/GROWTH FACTOR RECEPTOR / Nuclear Receptor / Coactivator / Ligand / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
Function / homology | ![]() Generic Transcription Pathway / nuclear receptor binding => GO:0016922 / Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of intracellular receptors ...Generic Transcription Pathway / nuclear receptor binding => GO:0016922 / Transcriptional regulation of granulopoiesis / Carnitine metabolism / Transcriptional regulation of white adipocyte differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of intracellular receptors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / ventricular cardiac muscle cell differentiation / visceral serous pericardium development / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / embryonic eye morphogenesis / mesenchyme development / positive regulation of translational initiation by iron / Endogenous sterols / glandular epithelial cell development / maternal placenta development / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / growth plate cartilage development / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / G0 to G1 transition / thyroid hormone receptor signaling pathway / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / negative regulation of cartilage development / multicellular organism development / Regulation of lipid metabolism by PPARalpha / retinoic acid-responsive element binding / core mediator complex / regulation of vitamin D receptor signaling pathway / Cytoprotection by HMOX1 / embryonic digestive tract development / positive regulation of thyroid hormone receptor signaling pathway / Estrogen-dependent gene expression / angiogenesis involved in coronary vascular morphogenesis / striatum development / cardiac muscle cell differentiation / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / nuclear retinoic acid receptor binding / mediator complex / positive regulation of keratinocyte differentiation / embryonic heart tube development / camera-type eye development / neural precursor cell proliferation / cellular response to thyroid hormone stimulus / positive regulation of programmed cell death / positive regulation of vitamin D receptor signaling pathway / positive regulation of hepatocyte proliferation / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis / nuclear vitamin D receptor binding / peroxisome proliferator activated receptor binding / lens development in camera-type eye / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / nuclear thyroid hormone receptor binding / mammary gland epithelial cell proliferation / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / regulation of myelination / ureteric bud development / megakaryocyte development / nuclear steroid receptor activity / histone acetyltransferase binding / cellular response to steroid hormone stimulus / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to hepatocyte growth factor stimulus / regulation of branching involved in prostate gland morphogenesis / LBD domain binding / epithelial cell proliferation involved in mammary gland duct elongation / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / transcription factor binding / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / retinoic acid receptor signaling pathway / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / positive regulation of bone mineralization / nuclear retinoid X receptor binding / heart morphogenesis / nuclear receptor-mediated steroid hormone signaling pathway / response to retinoic acid Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pogenberg, V. / Guichou, J.F. / Vivat-Hannah, V. / Kammerer, S. / Perez, E. / Germain, P. / De Lera, A.R. / Gronemeyer, H. / Royer, C.A. / Bourguet, W. | ||||||
![]() | ![]() Title: CHARACTERIZATION OF THE INTERACTION BETWEEN RAR/RXR HETERODIMERS AND TRANSCRIPTIONAL COACTIVATORS THROUGH STRUCTURAL AND FLUORESCENCE ANISOTROPY STUDIES Authors: Pogenberg, V. / Guichou, J.F. / Vivat-Hannah, V. / Kammerer, S. / Perez, E. / Germain, P. / De Lera, A.R. / Gronemeyer, H. / Royer, C.A. / Bourguet, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.2 KB | Display | ![]() |
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PDB format | ![]() | 161.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 46.4 KB | Display | |
Data in CIF | ![]() | 61.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dkfS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components
#1: Protein | Mass: 26579.727 Da / Num. of mol.: 2 / Fragment: Ligand-Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 33978.113 Da / Num. of mol.: 2 / Fragment: Ligand-Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 1609.910 Da / Num. of mol.: 4 / Fragment: Nuclear Receptor Box 2 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse). References: UniProt: Q8BX19, UniProt: Q925J9*PLUS #4: Chemical | ChemComp-9CR / ( #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.5 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: PEG 3350, Sodium Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 19, 2003 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→36.21 Å / Num. obs: 42989 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 92 Å2 / Rsym value: 0.083 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.38 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: TRUNCATED VERSION OF PDB ENTRY 1DKF Resolution: 2.9→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Bsol: 53.7918 Å2 / ksol: 0.345913 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.56 Å / Luzzati sigma a free: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |