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- PDB-3plv: Structure of Hub-1 protein in complex with Snu66 peptide (HINDII) -
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Open data
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Basic information
Entry | Database: PDB / ID: 3plv | ||||||
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Title | Structure of Hub-1 protein in complex with Snu66 peptide (HINDII) | ||||||
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![]() | PEPTIDE BINDING PROTEIN / Ubiquitin-like | ||||||
Function / homology | ![]() cell morphogenesis involved in conjugation with cellular fusion / maturation of 5S rRNA / mRNA cis splicing, via spliceosome / U4/U6 x U5 tri-snRNP complex / post-translational protein modification / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / protein tag activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mishra, S.K. / Ammon, T. / Popowicz, G.M. / Krajewski, M. / Nagel, R.J. / Ares, M. / Holak, T.A. / Jentsch, S. | ||||||
![]() | ![]() Title: Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Authors: Mishra, S.K. / Ammon, T. / Popowicz, G.M. / Krajewski, M. / Nagel, R.J. / Ares, M. / Holak, T.A. / Jentsch, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.2 KB | Display | ![]() |
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PDB format | ![]() | 23.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.6 KB | Display | ![]() |
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Full document | ![]() | 432.6 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pluC ![]() 1ubiS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 10440.913 Da / Num. of mol.: 1 / Mutation: A20G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HUB1, YNR032C-A / Plasmid: pET-28 / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 2282.634 Da / Num. of mol.: 1 / Fragment: HINDII domain / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.2M Ammonium Iodide, 20% PEG 3350, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 9, 2006 / Details: mirrors |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45 Å / Num. all: 9009 / Num. obs: 8959 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 9.96 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1UBI Resolution: 1.9→41.78 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / SU B: 3.91 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.774 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→41.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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