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- PDB-1mvc: Crystal structure of the human RXR alpha ligand binding domain bo... -
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Basic information
Entry | Database: PDB / ID: 1mvc | ||||||
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Title | Crystal structure of the human RXR alpha ligand binding domain bound to the synthetic agonist compound BMS 649 and a coactivator peptide | ||||||
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![]() | TRANSCRIPTION / Nuclear Receptor / Retinoic Acid / Agonist recognition / Transcription Factor | ||||||
Function / homology | ![]() 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 receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex ...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 receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / 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 / response to retinoic acid / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / HATs acetylate histones / double-stranded DNA binding / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription regulator complex / transcription coactivator activity / cell differentiation / receptor complex / nuclear body / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Egea, P.F. / Mitschler, A. / Moras, D. | ||||||
![]() | ![]() Title: Molecular Recognition of Agonist Ligands by RXRs Authors: Egea, P.F. / Mitschler, A. / Moras, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.3 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.2 KB | Display | ![]() |
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Full document | ![]() | 460.7 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mv9C ![]() 1mznC ![]() 1fbyS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Details | Although the asymmetric unit contains one monomer of the RXR-peptide-BMS649 complex, The biological assembly is an homodimer generated by the crystallographic two fold axis |
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Components
#1: Protein | Mass: 26856.039 Da / Num. of mol.: 1 / Fragment: ligand binding domain(residues 223-462) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 1 / Fragment: NR box / Source method: obtained synthetically Details: the GRIP1 NR1 coactivator peptide has been synthetized by automatic chemical synthesis References: UniProt: Q15596 |
#3: Chemical | ChemComp-BM6 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, NaCl, Glycerol, BisTris, Pipes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 82137 / Num. obs: 81070 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.076 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 9.3 / Num. unique all: 1717 / Rsym value: 0.093 / % possible all: 93.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 19091 / Num. measured all: 81070 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS Lowest resolution: 2 Å / % possible obs: 93.5 % / Rmerge(I) obs: 0.093 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB id 1FBY Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 17234 / % reflection Rfree: 7.5 % / Rfactor all: 0.228 / Rfactor obs: 0.201 / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.201 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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