+Open data
-Basic information
Entry | Database: PDB / ID: 3tkn | ||||||
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Title | Structure of the Nup82-Nup159-Nup98 heterotrimer | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / protein complex / oncoprotein | ||||||
Function / homology | Function and homology information Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore linkers / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / nuclear pore localization / adenyl-nucleotide exchange factor activity / nuclear pore central transport channel / RHO GTPases Activate Formins / nuclear pore outer ring / Separation of Sister Chromatids / nuclear pore complex assembly / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear inclusion body / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / positive regulation of mRNA splicing, via spliceosome / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / mRNA transport / mRNA export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / protein export from nucleus / serine-type peptidase activity / nuclear periphery / peptide binding / promoter-specific chromatin binding / protein import into nucleus / transcription corepressor activity / nuclear envelope / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / intracellular membrane-bounded organelle / mRNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Stuwe, T.T. / Hoelz, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Molecular basis for the anchoring of proto-oncoprotein nup98 to the cytoplasmic face of the nuclear pore complex. Authors: Stuwe, T. / Schada von Borzyskowski, L. / Davenport, A.M. / Hoelz, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tkn.cif.gz | 370.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tkn.ent.gz | 303.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tkn_validation.pdf.gz | 508.9 KB | Display | wwPDB validaton report |
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Full document | 3tkn_full_validation.pdf.gz | 613.8 KB | Display | |
Data in XML | 3tkn_validation.xml.gz | 75.3 KB | Display | |
Data in CIF | 3tkn_validation.cif.gz | 100.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/3tkn ftp://data.pdbj.org/pub/pdb/validation_reports/tk/3tkn | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 51607.301 Da / Num. of mol.: 3 / Fragment: UNP residues 1-452 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HRB187, J1135, NUP82, YJL061W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P40368 #2: Protein/peptide | Mass: 4319.120 Da / Num. of mol.: 3 / Fragment: UNP residues 1425-1460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP158, NUP159, RAT7, YIL115C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P40477 #3: Protein | Mass: 17116.346 Da / Num. of mol.: 3 / Fragment: UNP residues 732-880 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nup98 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q6PFD9 |
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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: 3.12 Å3/Da / Density % sol: 60.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18.5% PEG3350, 100 mM potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→20 Å / Num. all: 37089 / Num. obs: 34404 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.018 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 33.0094 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 199.47 Å2 / Biso mean: 113.9914 Å2 / Biso min: 58.55 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→20 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: CNS_TOPPAR:protein_rep.param |