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Open data
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Basic information
Entry | Database: PDB / ID: 1q1t | ||||||
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Title | Mouse Importin alpha: non-phosphorylated SV40 CN peptide complex | ||||||
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![]() | PROTEIN TRANSPORT / importin alpha/karyopherin alpha / nuclear localisation sequence (NLS) recognition / phosphorylation / simian virus (SV40) large tumor-antigen (T-antigen) NLS / X-ray crystal structure | ||||||
Function / homology | ![]() symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / bidirectional double-stranded viral DNA replication / NLS-dependent protein nuclear import complex / viral DNA genome replication / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / bidirectional double-stranded viral DNA replication / NLS-dependent protein nuclear import complex / viral DNA genome replication / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / protein import into nucleus / host cell / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA-binding transcription factor binding / postsynaptic density / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / glutamatergic synapse / host cell nucleus / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fontes, M.R.M. / Teh, T. / Toth, G. / John, A. / Pavo, I. / Jans, D.A. / Kobe, B. | ||||||
![]() | ![]() Title: Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-alpha Authors: Fontes, M.R.M. / Teh, T. / Toth, G. / John, A. / Pavo, I. / Jans, D.A. / Kobe, B. #1: ![]() Title: Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin alpha Authors: Fontes, M.R.M. / Teh, T. / Kobe, B. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106 KB | Display | ![]() |
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PDB format | ![]() | 79.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
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Full document | ![]() | 451.8 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1q1sC ![]() 1ialS S: Starting model for refinement C: citing same article ( |
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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/peptide | Mass: 2685.940 Da / Num. of mol.: 2 / Fragment: CN peptide / Mutation: S120A, S123A, T124A / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN SIMIAN VIRUS 40 (SV40) LARGE TUMOR-ANTIGEN References: UniProt: P03070 #2: Protein | | Mass: 50461.285 Da / Num. of mol.: 1 / Fragment: NLS binding domain (70-529) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.24 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: Sodium Citrate, DTT, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / PH range low: 6.5 / PH range high: 6 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 13, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→99 Å / Num. all: 25902 / Num. obs: 25902 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 17.1 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.9 / % possible all: 88.6 |
Reflection | *PLUS Num. measured all: 443936 |
Reflection shell | *PLUS % possible obs: 88.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IAL Resolution: 2.5→29.62 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.7542 Å2 / ksol: 0.358481 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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