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- PDB-1ko6: Crystal Structure of C-terminal Autoproteolytic Domain of Nucleop... -
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Basic information
Entry | Database: PDB / ID: 1ko6 | ||||||
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Title | Crystal Structure of C-terminal Autoproteolytic Domain of Nucleoporin Nup98 | ||||||
![]() | (Nuclear Pore Complex Protein Nup98) x 2 | ||||||
![]() | TRANSFERASE / nucleoporin / autoproteolysis / nuclear pore | ||||||
Function / homology | ![]() telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus ...telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / positive regulation of mRNA splicing, via spliceosome / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / molecular condensate scaffold activity / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / Separation of Sister Chromatids / protein import into nucleus / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hodel, A.E. / Hodel, M.R. / Griffis, E.R. / Hennig, K.A. / Ratner, G.A. / Songli, X. / Powers, M.A. | ||||||
![]() | ![]() Title: The three-dimensional structure of the autoproteolytic, nuclear pore-targeting domain of the human nucleoporin Nup98. Authors: Hodel, A.E. / Hodel, M.R. / Griffis, E.R. / Hennig, K.A. / Ratner, G.A. / Xu, S. / Powers, M.A. | ||||||
History |
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Remark 999 | SEQUENCE Chains A(C) and B(D) are autocatalytically cleaved between residues 863 and 864. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 67.6 KB | Display | ![]() |
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PDB format | ![]() | 49 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 392.3 KB | Display | ![]() |
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Full document | ![]() | 416.3 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21201.639 Da / Num. of mol.: 2 Fragment: C-terminal Autoproteolytic Domain (Sequence database residues 677-863) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 7111.907 Da / Num. of mol.: 2 Fragment: C-terminal Autoproteolytic Domain (Sequence database residues 864-920) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66.05 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.75 Details: MgCl, PEG8000, Tris, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 41000 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 |
Reflection shell | Highest resolution: 2.8 Å |
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Processing
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Refinement | Method to determine structure: ![]() ![]()
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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LS refinement shell | Highest resolution: 3 Å | ||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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