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Yorodumi- PDB-4cn3: Crystal Structure of the Human Retinoid X Receptor DNA-Binding Do... -
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-Basic information
Entry | Database: PDB / ID: 4cn3 | ||||||
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Title | Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Gde1SpA Response Element | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism ...DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Synthesis of bile acids and bile salts / hormone-mediated signaling pathway / peroxisome proliferator activated 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 / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / transcription coregulator binding / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / Heme signaling / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / receptor complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | McEwen, A.G. / Poussin-Courmontagne, P. / Osz, J. / Rochel, N. | ||||||
Citation | Journal: Sci.Rep. / Year: 2015 Title: Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor. Authors: Osz, J. / Mcewen, A.G. / Poussin-Courmontagne, P. / Moutier, E. / Birck, C. / Davidson, I. / Moras, D. / Rochel, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cn3.cif.gz | 220.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cn3.ent.gz | 173.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cn3_validation.pdf.gz | 475 KB | Display | wwPDB validaton report |
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Full document | 4cn3_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 4cn3_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 4cn3_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/4cn3 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cn3 | HTTPS FTP |
-Related structure data
Related structure data | 4cn2C 4cn5C 4cn7C 1dszS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-RETINOIC ACID RECEPTOR RXR- ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 10262.926 Da / Num. of mol.: 3 / Fragment: DNA-BINDING DOMAIN, RESIDUES 130-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHXGW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19793 #2: Protein | | Mass: 10263.910 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 130-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHXGW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19793 |
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-DNA chain , 2 types, 4 molecules EGFH
#3: DNA chain | Mass: 5170.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) #4: DNA chain | Mass: 5241.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) |
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-Non-polymers , 2 types, 331 molecules
#5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 46.1 % / Description: NONE |
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Crystal grow | pH: 6.11 / Details: 20% PEG 3350, 0.2M NH4CL, pH 6.11 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 19, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→69.6 Å / Num. obs: 23573 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 41.34 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.5 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DSZ Resolution: 2.35→24.57 Å / Cor.coef. Fo:Fc: 0.9114 / Cor.coef. Fo:Fc free: 0.8842 / SU R Cruickshank DPI: 0.507 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.052 / SU Rfree Blow DPI: 0.289 / SU Rfree Cruickshank DPI: 0.273 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4303. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4303. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
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Displacement parameters | Biso mean: 28.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.268 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→24.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.48 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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