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Yorodumi- PDB-4q9t: Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propel... -
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-Basic information
Entry | Database: PDB / ID: 4q9t | ||||||
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Title | Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propeller domain | ||||||
Components | Nucleoporin NUP133 | ||||||
Keywords | PROTEIN TRANSPORT / Nuclear Pore Complex / Nucleoporin / Nup84 complex / ALPS motif / Structural genomics / PSI-Biology / Nucleocytoplasmic Transport: a Target for Cellular Control / NPCXstals / New York SGX Research Center for Structural Genomics / NYSGXRC / Nup133 / Beta-propeller domain / and New York Structural Genomics Research Center / NYSGRC / Protein Structure Initiative / New York Structural Genomics Research Consortium | ||||||
Function / homology | Function and homology information nuclear pore localization => GO:0051664 / mRNA export from nucleus in response to heat stress / nuclear pore outer ring / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / tRNA export from nucleus / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / subtelomeric heterochromatin formation ...nuclear pore localization => GO:0051664 / mRNA export from nucleus in response to heat stress / nuclear pore outer ring / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / tRNA export from nucleus / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / subtelomeric heterochromatin formation / protein import into nucleus / double-strand break repair / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / membrane / cytosol Similarity search - Function | ||||||
Biological species | Vanderwaltozyma polyspora (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Sampathkumar, P. / Bonanno, J.B. / Almo, S.C. / Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals) / New York SGX Research Center for Structural Genomics (NYSGXRC) / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: to be published Title: Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propeller domain Authors: Sampathkumar, P. / Bonanno, J.B. / Rout, M.P. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q9t.cif.gz | 314.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q9t.ent.gz | 270.6 KB | Display | PDB format |
PDBx/mmJSON format | 4q9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q9t_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 4q9t_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 4q9t_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 4q9t_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/4q9t ftp://data.pdbj.org/pub/pdb/validation_reports/q9/4q9t | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 51860.855 Da / Num. of mol.: 2 / Fragment: Beta-propeller domain residues 55-502 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vanderwaltozyma polyspora (fungus) / Strain: DSM 70294 / Gene: Kpol_1018p77, Nup133 / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-Plus-RIL / References: UniProt: A7TDS5 |
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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: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: Protein (10 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT), Reservoir (100mM Hepes pH 8.2, 10% PEG 3350, 100mM Ammonium Sulfate), Cryoprotection (30% Glycerol), VAPOR DIFFUSION, ...Details: Protein (10 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT), Reservoir (100mM Hepes pH 8.2, 10% PEG 3350, 100mM Ammonium Sulfate), Cryoprotection (30% Glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-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: Oct 21, 2008 / Details: MIRRORS |
Radiation | Monochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 20381 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 88.3 Å2 / Rmerge(I) obs: 0.189 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.02542 / Mean I/σ(I) obs: 1.2 / Num. unique all: 3224 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 59.442 / SU ML: 0.439 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 191.8 Å2 / Biso mean: 101.079 Å2 / Biso min: 62.93 Å2
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Refinement step | Cycle: LAST / Resolution: 3→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 22068 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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