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- PDB-1pjm: Mouse Importin alpha-bipartite NLS from human retinoblastoma prot... -
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Basic information
Entry | Database: PDB / ID: 1pjm | ||||||
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Title | Mouse Importin alpha-bipartite NLS from human retinoblastoma protein Complex | ||||||
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![]() | PROTEIN TRANSPORT / IMPORTIN ALPHA/KARYOPHERIN ALPHA / NUCLEAR LOCALIZATION SEQUENCE (NLS) RECOGNITION / BIPARTITE NLS / HUMAN RETINOBLASTOMA PROTEIN | ||||||
Function / homology | ![]() Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / positive regulation of extracellular matrix organization / Sensing of DNA Double Strand Breaks / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of centromere complex assembly / positive regulation of macrophage differentiation / entry of viral genome into host nucleus through nuclear pore complex via importin / glial cell apoptotic process / tissue homeostasis / positive regulation of viral life cycle / protein localization to chromosome, centromeric region / negative regulation of protein serine/threonine kinase activity / positive regulation of mitotic metaphase/anaphase transition / importin-alpha family protein binding / negative regulation of hepatocyte apoptotic process / positive regulation of transcription regulatory region DNA binding / NLS-dependent protein nuclear import complex / neuron maturation / postsynapse to nucleus signaling pathway / digestive tract development / aortic valve morphogenesis / Replication of the SARS-CoV-1 genome / myoblast differentiation / negative regulation of cold-induced thermogenesis / SWI/SNF complex / nuclear import signal receptor activity / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / nuclear localization sequence binding / smoothened signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / NLS-bearing protein import into nucleus / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / hepatocyte apoptotic process / skeletal muscle cell differentiation / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / chromosome organization / glial cell proliferation / chondrocyte differentiation / Nuclear events stimulated by ALK signaling in cancer / heterochromatin formation / Cyclin E associated events during G1/S transition / negative regulation of smoothened signaling pathway / Cyclin A:Cdk2-associated events at S phase entry / striated muscle cell differentiation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / epithelial cell proliferation / phosphoprotein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of protein kinase activity / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Oncogene Induced Senescence / negative regulation of DNA-binding transcription factor activity / negative regulation of cell growth / PML body / kinase binding / negative regulation of inflammatory response / cytoplasmic stress granule / spindle / G1/S transition of mitotic cell cycle / cellular response to insulin stimulus / protein import into nucleus / transcription corepressor activity / Cyclin D associated events in G1 / negative regulation of epithelial cell proliferation / neuron projection development / host cell / disordered domain specific binding / cellular response to xenobiotic stimulus / Replication of the SARS-CoV-2 genome / spermatogenesis / DNA-binding transcription factor binding / neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / Ras protein signal transduction / molecular adaptor activity / postsynaptic density / cell differentiation / regulation of cell cycle / chromatin remodeling / cell division / negative regulation of gene expression / negative regulation of DNA-templated transcription / glutamatergic synapse Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / Kobe, B. | ||||||
![]() | ![]() Title: Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha Authors: Fontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / 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. #2: ![]() Title: Biophysical Characterization of Interactions Involving Impostin-alpha during Nuclear Import Authors: Catimel, B. / Teh, T. / Fontes, M.R.M. / Jennings, I.G. / Jans, D. / Howlett, G.J. / Nice, E.C. / Kobe, B. #3: ![]() Title: Autoinhibition by an internal nuclear localization signal reveled by the crystal structure of mammalian importin alpha Authors: Kobe, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.2 KB | Display | ![]() |
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PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 448.2 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pjnC ![]() 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: 2129.530 Da / Num. of mol.: 1 Fragment: NLS (nuclear localization signal) bipartite peptide Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN HUMAN RETINOBLASTOMA PROTEIN References: UniProt: P06400 |
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#2: Protein | Mass: 49886.633 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 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.01 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Sodium Citrate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
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: Aug 10, 2000 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→99 Å / Num. all: 25382 / Num. obs: 25382 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.8 / % possible all: 98.3 |
Reflection | *PLUS % possible obs: 96 % / Num. measured all: 249870 |
Reflection shell | *PLUS % possible obs: 98.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY: 1ial Resolution: 2.5→29.57 Å / Rfactor Rfree error: 0.007 / 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: 38.52 Å2 / ksol: 0.363607 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / 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: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.263 |