+Open data
-Basic information
Entry | Database: PDB / ID: 1ovl | ||||||
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Title | Crystal Structure of Nurr1 LBD | ||||||
Components | (Orphan nuclear receptor NURR1 (MSE ...) x 2 | ||||||
Keywords | TRANSCRIPTION / Nuur1 / LBD | ||||||
Function / homology | Function and homology information general adaptation syndrome / habenula development / cellular response to corticotropin-releasing hormone stimulus / central nervous system neuron differentiation / central nervous system projection neuron axonogenesis / nuclear glucocorticoid receptor binding / regulation of dopamine metabolic process / midbrain dopaminergic neuron differentiation / regulation of respiratory gaseous exchange / dopaminergic neuron differentiation ...general adaptation syndrome / habenula development / cellular response to corticotropin-releasing hormone stimulus / central nervous system neuron differentiation / central nervous system projection neuron axonogenesis / nuclear glucocorticoid receptor binding / regulation of dopamine metabolic process / midbrain dopaminergic neuron differentiation / regulation of respiratory gaseous exchange / dopaminergic neuron differentiation / neuron maturation / dopamine biosynthetic process / fat cell differentiation / negative regulation of apoptotic signaling pathway / canonical Wnt signaling pathway / nuclear retinoid X receptor binding / response to amphetamine / post-embryonic development / adult locomotory behavior / neuron migration / SUMOylation of intracellular receptors / beta-catenin binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / negative regulation of neuron apoptotic process / transcription regulator complex / transcription by RNA polymerase II / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Wang, Z. / Liu, J. / Walker, N. | ||||||
Citation | Journal: Nature / Year: 2003 Title: Structure and Function of Nurr1 identifies a Class of Ligand-Independent Nuclear Receptors Authors: Wang, Z. / Benoit, G. / Liu, J. / Prasad, S. / Aarnisalo, P. / Liu, X. / Xu, H. / Walker, N. / Perlmann, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ovl.cif.gz | 295.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ovl.ent.gz | 237.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ovl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ovl_validation.pdf.gz | 414 KB | Display | wwPDB validaton report |
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Full document | 1ovl_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 1ovl_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 1ovl_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/1ovl ftp://data.pdbj.org/pub/pdb/validation_reports/ov/1ovl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Orphan nuclear receptor NURR1 (MSE ... , 2 types, 6 molecules ADBCEF
#1: Protein | Mass: 30670.041 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2 OR NURR1 OR TINUR OR NOT / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P43354 #2: Protein | Mass: 30716.936 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2 OR NURR1 OR TINUR OR NOT / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P43354 |
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-Non-polymers , 4 types, 590 molecules
#3: Chemical | ChemComp-K / #4: Chemical | ChemComp-BR / #5: Chemical | ChemComp-IOD / | #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 2.3 Å3/Da / Density % sol: 46.54 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: PEG3350,KBr, Hepes, pH 6.5, VAPOR DIFFUSION, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.9 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2001 |
Radiation | Monochromator: Double cyrstal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→34.7 Å / Num. all: 287222 / Num. obs: 82388 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.072 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.4 / % possible all: 91.7 |
Reflection | *PLUS Num. measured all: 287222 / Rmerge(I) obs: 0.072 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→500 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |