+Open data
-Basic information
Entry | Database: PDB / ID: 5yd6 | ||||||
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Title | Crystal structure of PG-bound Nurr1-LBD | ||||||
Components | Nuclear receptor subfamily 4 group A member 2 | ||||||
Keywords | TRANSCRIPTION / NURR1 / LBD / PROSTAGLANDIN / MICHAEL ADDITION | ||||||
Function / homology | Function and homology information general adaptation syndrome / habenula development / central nervous system neuron differentiation / cellular response to corticotropin-releasing hormone stimulus / central nervous system projection neuron axonogenesis / regulation of dopamine metabolic process / : / midbrain dopaminergic neuron differentiation / nuclear glucocorticoid receptor binding / regulation of respiratory gaseous exchange ...general adaptation syndrome / habenula development / central nervous system neuron differentiation / cellular response to corticotropin-releasing hormone stimulus / central nervous system projection neuron axonogenesis / regulation of dopamine metabolic process / : / midbrain dopaminergic neuron differentiation / nuclear glucocorticoid receptor binding / 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 / adult locomotory behavior / post-embryonic development / 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 / signal transduction / 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 / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Sreekanth, R. / Yoon, H.S. | ||||||
Citation | Journal: To Be Published Title: Structure of Nurr1 bound to cyclopentenone prostaglandin A2 and its mechanism of action in ameliorating dopaminergic neurodegeneration in Drosophila Authors: Rajan, S. / Toh, H.T. / Lim, K.H. / Yoon, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yd6.cif.gz | 381.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yd6.ent.gz | 312.8 KB | Display | PDB format |
PDBx/mmJSON format | 5yd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yd6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5yd6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5yd6_validation.xml.gz | 38 KB | Display | |
Data in CIF | 5yd6_validation.cif.gz | 52.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/5yd6 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/5yd6 | HTTPS FTP |
-Related structure data
Related structure data | 1ovlS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 30576.256 Da / Num. of mol.: 4 / Fragment: UNP residues 328-598 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2, NOT, NURR1, TINUR / Plasmid: PET-SUMO / Production host: Escherichia coli (E. coli) / References: UniProt: P43354 #2: Chemical | ChemComp-8SU / (~{ #3: Chemical | #4: 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: 2.24 Å3/Da / Density % sol: 45.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, MES PH 5.5 AND MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→94.08 Å / Num. obs: 46996 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.34→2.47 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6778 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OVL Resolution: 2.34→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 19.847 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.265
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.042 Å2
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Refinement step | Cycle: 1 / Resolution: 2.34→20 Å
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Refine LS restraints |
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