+Open data
-Basic information
Entry | Database: PDB / ID: 3plu | ||||||
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Title | Structure of Hub-1 protein in complex with Snu66 peptide (HINDI) | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / Ubiquitin-like / HUB-1 / Snu66 | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Mishra, S.K. / Ammon, T. / Popowicz, G.M. / Krajewski, M. / Nagel, R.J. / Ares, M. / Holak, T.A. / Jentsch, S. | ||||||
Citation | Journal: Nature / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3plu.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3plu.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 3plu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3plu_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 3plu_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 3plu_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3plu_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/3plu ftp://data.pdbj.org/pub/pdb/validation_reports/pl/3plu | HTTPS FTP |
-Related structure data
Related structure data | 3plvC 1ubiS 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: 10440.913 Da / Num. of mol.: 2 / Mutation: A20G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HUB1, YNR032C-A / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q6Q546 #2: Protein/peptide | Mass: 2217.562 Da / Num. of mol.: 2 / Fragment: HINDI domain / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12420 #3: 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: 1.84 Å3/Da / Density % sol: 33.26 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 20% PEG 3350, 0.2M Ammonium Chloride, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
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: 1.4→30 Å / Num. all: 35599 / Num. obs: 33677 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.4→1.5 Å / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 5.56 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1UBI Resolution: 1.4→26.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.433 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.077 / 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: 18.696 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→26.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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