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Yorodumi- PDB-4b18: The crystal structure of human Importin alpha 5 with TERT NLS peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b18 | ||||||
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Title | The crystal structure of human Importin alpha 5 with TERT NLS peptide | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / PEPTIDE / TRANSPORT PROTEIN - PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / Inhibition of nitric oxide production / telomerase catalytic core complex ...satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / Inhibition of nitric oxide production / telomerase catalytic core complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase activity / telomerase RNA reverse transcriptase activity / RNA-templated DNA biosynthetic process / regulation of DNA recombination / establishment of protein localization to telomere / Transport of Ribonucleoproteins into the Host Nucleus / nuclear telomere cap complex / siRNA processing / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / postsynapse to nucleus signaling pathway / telomerase RNA binding / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / regulation of canonical Wnt signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / telomeric DNA binding / DNA biosynthetic process / RNA-templated transcription / positive regulation of stem cell proliferation / mitochondrial nucleoid / Vpr-mediated nuclear import of PICs / Integration of provirus / negative regulation of cellular senescence / Telomere Extension By Telomerase / positive regulation of Wnt signaling pathway / telomere maintenance via telomerase / replicative senescence / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of G1/S transition of mitotic cell cycle / response to cadmium ion / negative regulation of endothelial cell apoptotic process / nuclear pore / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / mitochondrion organization / Assembly of the ORC complex at the origin of replication / positive regulation of nitric-oxide synthase activity / positive regulation of glucose import / Formation of the beta-catenin:TCF transactivating complex / regulation of protein stability / transcription coactivator binding / PML body / ISG15 antiviral mechanism / positive regulation of miRNA transcription / protein import into nucleus / RNA-directed DNA polymerase / positive regulation of angiogenesis / RNA-directed DNA polymerase activity / Interferon alpha/beta signaling / positive regulation of protein binding / cellular response to hypoxia / protein-folding chaperone binding / regulation of apoptotic process / negative regulation of neuron apoptotic process / tRNA binding / postsynaptic density / chromosome, telomeric region / nuclear speck / negative regulation of gene expression / RNA-dependent RNA polymerase activity / glutamatergic synapse / dendrite / nucleolus / protein homodimerization activity / DNA binding / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Kim, K.L. / Yoo, J.H. / Cho, H.S. | ||||||
Citation | Journal: J.Cell.Sci. / Year: 2015 Title: Akt-Mediated Phosphorylation Increases the Binding Affinity of Htert for Importin Alpha to Promote Nuclear Translocation. Authors: Jeong, S.A. / Kim, K. / Lee, J.H. / Cha, J.S. / Khadka, P. / Cho, H. / Chung, I.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b18.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b18.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 4b18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/4b18 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/4b18 | HTTPS FTP |
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-Related structure data
Related structure data | 2jdqS 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 | Mass: 49401.328 Da / Num. of mol.: 1 / Fragment: RESIDUES 66-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): CODON PLUS / References: UniProt: P52294 |
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#2: Protein/peptide | Mass: 2282.704 Da / Num. of mol.: 1 / Fragment: TERT NLS PEPTIDE, RESIDUES 222-240 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O14746, RNA-directed DNA polymerase |
#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: 3.19 Å3/Da / Density % sol: 61.44 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 77.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50 Å / Num. obs: 21441 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 2.56→2.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 2 / % possible all: 96.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JDQ Resolution: 2.52→70 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.026 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.958 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→70 Å
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Refine LS restraints |
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