+Open data
-Basic information
Entry | Database: PDB / ID: 1q1s | ||||||
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Title | Mouse Importin alpha- phosphorylated SV40 CN peptide complex | ||||||
Components |
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Keywords | 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 | Function and homology information 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 / postsynapse to nucleus signaling pathway / viral DNA genome replication / DNA 3'-5' helicase / nuclear import signal receptor activity ...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 / postsynapse to nucleus signaling pathway / viral DNA genome replication / DNA 3'-5' helicase / 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 / cytoplasmic stress granule / protein import into nucleus / host cell / double-stranded DNA binding / single-stranded DNA binding / DNA-binding transcription factor binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / postsynaptic density / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / hydrolase activity / 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Fontes, M.R.M. / Teh, T. / Toth, G. / John, A. / Pavo, I. / Jans, D.A. / Kobe, B. | ||||||
Citation | Journal: Biochem.J. / Year: 2003 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: Journal: J.Mol.Biol. / Year: 2000 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q1s.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q1s.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 1q1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q1s_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 1q1s_full_validation.pdf.gz | 460.5 KB | Display | |
Data in XML | 1q1s_validation.xml.gz | 23 KB | Display | |
Data in CIF | 1q1s_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/1q1s ftp://data.pdbj.org/pub/pdb/validation_reports/q1/1q1s | HTTPS FTP |
-Related structure data
Related structure data | 1q1tC 1ialS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2602.746 Da / Num. of mol.: 2 / Fragment: CN peptide - Ser112 chemically phosphorylated / 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. Ser112 WAS CHEMICALLY PHOSPHORYLATED 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.) Mus musculus (house mouse) / Gene: KPNA2 OR RCH1 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P03070, UniProt: P52293*PLUS #3: Water | ChemComp-HOH / | |
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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: 3.17 Å3/Da / Density % sol: 61.15 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Sodium Citrate, DTT, pH 6.5, 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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 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: 2.3→99 Å / Num. all: 32147 / Num. obs: 32147 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 5.3 / % possible all: 95.8 |
Reflection | *PLUS Num. measured all: 272363 |
Reflection shell | *PLUS % possible obs: 95.8 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1IAL Resolution: 2.3→28.65 Å / Rfactor Rfree error: 0.005 / 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: 46.8322 Å2 / ksol: 0.372509 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→28.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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