+Open data
-Basic information
Entry | Database: PDB / ID: 3oqs | ||||||
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Title | Crystal structure of importin-alpha bound to a CLIC4 NLS peptide | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / importin alpha / karyopherin alpha / nuclear localisation signal (NLS) recognition / chloride intracellular channel 4 / CLIC4 NLS / Armadillo repeat / Nuclear import | ||||||
Function / homology | Function and homology information establishment or maintenance of apical/basal cell polarity / retina vasculature morphogenesis in camera-type eye / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / endothelial cell morphogenesis / positive regulation of viral life cycle / vacuolar acidification / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / fertilization ...establishment or maintenance of apical/basal cell polarity / retina vasculature morphogenesis in camera-type eye / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / endothelial cell morphogenesis / positive regulation of viral life cycle / vacuolar acidification / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / fertilization / host cell / chloride transport / nuclear import signal receptor activity / nuclear localization sequence binding / regulation of cytoskeleton organization / NLS-bearing protein import into nucleus / chloride channel activity / branching morphogenesis of an epithelial tube / microvillus / chloride channel complex / keratinocyte differentiation / cellular response to calcium ion / negative regulation of cell migration / multicellular organism growth / cytoplasmic vesicle membrane / nuclear matrix / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / cell-cell junction / actin cytoskeleton / apical part of cell / midbody / angiogenesis / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / cell differentiation / centrosome / glutamatergic synapse / perinuclear region of cytoplasm / cell surface / mitochondrion / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mynott, A.V. / Brown, L.J. / Harrop, S.J. / Curmi, P.M.G. | ||||||
Citation | Journal: Febs J. / Year: 2011 Title: Crystal structure of importin-alpha bound to a peptide bearing the nuclear localisation signal from chloride intracellular channel protein 4 Authors: Mynott, A.V. / Harrop, S.J. / Brown, L.J. / Breit, S.N. / Kobe, B. / Curmi, P.M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oqs.cif.gz | 188.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oqs.ent.gz | 148 KB | Display | PDB format |
PDBx/mmJSON format | 3oqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/3oqs ftp://data.pdbj.org/pub/pdb/validation_reports/oq/3oqs | HTTPS FTP |
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-Related structure data
Related structure data | 1ialS S: Starting model for refinement |
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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: 1208.495 Da / Num. of mol.: 1 Fragment: NLS (Nuclear Localisation Signal) UNP residues 198-207 Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y696 |
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#2: Protein | Mass: 55330.566 Da / Num. of mol.: 1 / Fragment: NLS Binding Domain (UNP residues 70-529) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52293 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.51 % / Mosaicity: 0.5 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.7M sodium citrate, 10mM DTT, 70mM HEPES pH 7.4, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→66.739 Å / Num. all: 46758 / Num. obs: 46758 / % possible obs: 96.7 % / Redundancy: 6.8 % / Rsym value: 0.096 / Net I/σ(I): 12.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IAL Resolution: 2→21.05 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.1846 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8499 / SU R Cruickshank DPI: 0.143 / SU Rfree: 0.1406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. SOLVENT MOLECULES WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. SOLVENT MOLECULES WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.38 Å2 / Biso mean: 36.2975 Å2 / Biso min: 10.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2→21.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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