+Open data
-Basic information
Entry | Database: PDB / ID: 4ys9 | |||||||||||||||||||||
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Title | Ataxin-3 Carboxy-Terminal Region - Crystal C1 (tetragonal) | |||||||||||||||||||||
Components | Maltose-binding periplasmic protein, Ataxin-3 chimera | |||||||||||||||||||||
Keywords | TRANSCRIPTION / Ataxin-3 / Polyglutamine / Huntington's Disease / Triplet repeat disorder / ataxins / ataxia | |||||||||||||||||||||
Function / homology | Function and homology information protein localization to cytosolic proteasome complex / regulation of cell-substrate adhesion / positive regulation of ERAD pathway / monoubiquitinated protein deubiquitination / intermediate filament cytoskeleton organization / protein K48-linked deubiquitination / nuclear inclusion body / positive regulation of ubiquitin-dependent protein catabolic process / protein K63-linked deubiquitination / cellular response to misfolded protein ...protein localization to cytosolic proteasome complex / regulation of cell-substrate adhesion / positive regulation of ERAD pathway / monoubiquitinated protein deubiquitination / intermediate filament cytoskeleton organization / protein K48-linked deubiquitination / nuclear inclusion body / positive regulation of ubiquitin-dependent protein catabolic process / protein K63-linked deubiquitination / cellular response to misfolded protein / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / protein quality control for misfolded or incompletely synthesized proteins / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of TORC1 signaling / cellular response to amino acid starvation / Josephin domain DUBs / nucleotide-excision repair / mitochondrial membrane / nuclear matrix / microtubule cytoskeleton organization / ATPase binding / nervous system development / outer membrane-bounded periplasmic space / cellular response to heat / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mitochondrial matrix / lysosomal membrane / ubiquitin protein ligase binding / synapse / nucleolus / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||||||||||||||
Authors | Zhemkov, V.A. / Kim, M. | |||||||||||||||||||||
Funding support | United States, Russian Federation, 6items
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Citation | Journal: FEBS Open Bio / Year: 2016 Title: The 2.2-Angstrom resolution crystal structure of the carboxy-terminal region of ataxin-3. Authors: Zhemkov, V.A. / Kulminskaya, A.A. / Bezprozvanny, I.B. / Kim, M. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ys9.cif.gz | 93.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ys9.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ys9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ys9_validation.pdf.gz | 848.3 KB | Display | wwPDB validaton report |
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Full document | 4ys9_full_validation.pdf.gz | 851.2 KB | Display | |
Data in XML | 4ys9_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4ys9_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/4ys9 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/4ys9 | HTTPS FTP |
-Related structure data
Related structure data | 4wthC 1anfS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48576.438 Da / Num. of mol.: 1 Fragment: MBP residues 27-392 (UNP) + Ataxin-3 C-terminal region (UNP residues 278-324) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: malE, Z5632, ECs5017, ATXN3, ATX3, MJD, MJD1, SCA3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEY0, UniProt: P54252 | ||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.12 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 25% PEG5000 MME, 1.0 M sodium acetate, 0.1 M imidazole, pH 8.0, 0.1 M zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2010 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.7 Å / Num. all: 31801 / Num. obs: 31801 / % possible obs: 99.8 % / Redundancy: 1.9 % / Rsym value: 0.053 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.2 / % possible all: 58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ANF Resolution: 2→59.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.921 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.834 Å2
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Refinement step | Cycle: LAST / Resolution: 2→59.67 Å
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