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Yorodumi- PDB-3kfo: Crystal structure of the C-terminal domain from the nuclear pore ... -
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-Basic information
Entry | Database: PDB / ID: 3kfo | ||||||
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Title | Crystal structure of the C-terminal domain from the nuclear pore complex component NUP133 from Saccharomyces cerevisiae | ||||||
Components | Nucleoporin NUP133 | ||||||
Keywords | PROTEIN TRANSPORT / Nuclear pore complex / NUP133 / yeast / proteolysis / STRUCTURAL GENOMICS / PSI2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / Membrane / mRNA transport / Nucleus / Phosphoprotein / Translocation / Transport / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information mRNA export from nucleus in response to heat stress / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus ...mRNA export from nucleus in response to heat stress / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / subtelomeric heterochromatin formation / nuclear pore / protein import into nucleus / double-strand break repair / nuclear envelope / nuclear membrane / chromosome, telomeric region / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Sampathkumar, P. / Bonanno, J.B. / Miller, S. / Bain, K. / Dickey, M. / Gheyi, T. / Almo, S.C. / Rout, M. / Sali, A. / Phillips, J. ...Sampathkumar, P. / Bonanno, J.B. / Miller, S. / Bain, K. / Dickey, M. / Gheyi, T. / Almo, S.C. / Rout, M. / Sali, A. / Phillips, J. / Pieper, U. / Fernandez-Martinez, J. / Franke, J.D. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex. Authors: Sampathkumar, P. / Gheyi, T. / Miller, S.A. / Bain, K.T. / Dickey, M. / Bonanno, J.B. / Kim, S.J. / Phillips, J. / Pieper, U. / Fernandez-Martinez, J. / Franke, J.D. / Martel, A. / Tsuruta, ...Authors: Sampathkumar, P. / Gheyi, T. / Miller, S.A. / Bain, K.T. / Dickey, M. / Bonanno, J.B. / Kim, S.J. / Phillips, J. / Pieper, U. / Fernandez-Martinez, J. / Franke, J.D. / Martel, A. / Tsuruta, H. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S.R. / Rout, M.P. / Sali, A. / Sauder, J.M. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kfo.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kfo.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/3kfo ftp://data.pdbj.org/pub/pdb/validation_reports/kf/3kfo | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33243.129 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 881-1157 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP133, RAT3, YKR082W, YKR402 / Plasmid: BC-pSGX3(BC); modified pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: P36161 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL RESIDUES ARE NOT DEFINED THE ELECTRON DENSITY DUE TO IN-CELL PROTEOLYSIS OF THE ...N-TERMINAL RESIDUES ARE NOT DEFINED THE ELECTRON DENSITY DUE TO IN-CELL PROTEOLYSI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 200mM Potassium Thiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 31, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→31 Å / Num. obs: 15683 / % possible obs: 99.7 % / Redundancy: 7.7 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.121 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 2236 / Rsym value: 0.414 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→23 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.489 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.165 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.49 Å2 / Biso mean: 23.975 Å2 / Biso min: 6.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→23 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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