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Yorodumi- PDB-2aiv: Multiple conformations in the ligand-binding site of the yeast nu... -
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-Basic information
Entry | Database: PDB / ID: 2aiv | ||||||
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Title | Multiple conformations in the ligand-binding site of the yeast nuclear pore targeting domain of NUP116P | ||||||
Components | fragment of Nucleoporin NUP116/NSP116 | ||||||
Keywords | TRANSPORT PROTEIN / Beta sandwich | ||||||
Function / homology | Function and homology information nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins ...nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / ribosomal large subunit export from nucleus / mRNA export from nucleus / nuclear pore / protein import into nucleus / nuclear envelope / ATPase binding / nuclear membrane / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Robinson, M.A. / Park, S. / Sun, Z.-Y.J. / Silver, P. / Wagner, G. / Hogle, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Multiple Conformations in the Ligand-binding Site of the Yeast Nuclear Pore-targeting Domain of Nup116p Authors: Robinson, M.A. / Park, S. / Sun, Z.-Y.J. / Silver, P.A. / Wagner, G. / Hogle, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aiv.cif.gz | 704.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aiv.ent.gz | 588.4 KB | Display | PDB format |
PDBx/mmJSON format | 2aiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aiv_validation.pdf.gz | 347.6 KB | Display | wwPDB validaton report |
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Full document | 2aiv_full_validation.pdf.gz | 583.2 KB | Display | |
Data in XML | 2aiv_validation.xml.gz | 71.6 KB | Display | |
Data in CIF | 2aiv_validation.cif.gz | 94.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/2aiv ftp://data.pdbj.org/pub/pdb/validation_reports/ai/2aiv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16808.256 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 967-1113 Source method: isolated from a genetically manipulated source Details: fragment Interacting with NUP82 NPC subcomplex Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP116, NSP116 / Plasmid: pDEST 15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q02630 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5-1mM Nup116p U-15N,13C Solvent system: 100mM sodium-potassium phosphate pH 6.5, 50mM NaCl, 1mM DTT, 90% H2O, 10% D2O |
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Sample conditions | Ionic strength: 100mM sodium-potassium phosphate pH 6.5, 50mM NaCl, 1mM DTT pH: 6.5 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 15 |