+Open data
-Basic information
Entry | Database: PDB / ID: 4wth | |||||||||||||||||||||
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Title | Ataxin-3 Carboxy Terminal Region - Crystal C2 (triclinic) | |||||||||||||||||||||
Components | Maltose-binding periplasmic protein, Ataxin-3 chimera | |||||||||||||||||||||
Keywords | TRANSCRIPTION / ataxin-3 / polyglutamine helix / nerve tissue proteins / polyQ / triplet repeat disorder | |||||||||||||||||||||
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 / detection of maltose stimulus / protein quality control for misfolded or incompletely synthesized proteins / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of TORC1 signaling / cellular response to amino acid starvation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / Josephin domain DUBs / nucleotide-excision repair / mitochondrial membrane / nuclear matrix / microtubule cytoskeleton organization / nervous system development / cellular response to heat / outer membrane-bounded periplasmic space / ATPase binding / 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 / periplasmic space / mitochondrial matrix / lysosomal membrane / synapse / DNA damage response / ubiquitin protein ligase binding / nucleolus / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 | 4wth.cif.gz | 326.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wth.ent.gz | 265.2 KB | Display | PDB format |
PDBx/mmJSON format | 4wth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/4wth ftp://data.pdbj.org/pub/pdb/validation_reports/wt/4wth | HTTPS FTP |
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-Related structure data
Related structure data | 4ys9C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48576.438 Da / Num. of mol.: 2 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, UniProt: P0AEX9*PLUS #2: Polysaccharide | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 24% PEG5000 MME, 0.9 M sodium acetate, 0.06 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: Oct 10, 2010 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution 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: 2.25→38.743 Å / Num. all: 41971 / Num. obs: 39115 / % possible obs: 94 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.25→2.36 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.2 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ANF Resolution: 2.25→77.79 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.067 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.244 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→77.79 Å
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