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- PDB-1m5n: Crystal structure of HEAT repeats (1-11) of importin b bound to t... -
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Basic information
Entry | Database: PDB / ID: 1m5n | ||||||
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Title | Crystal structure of HEAT repeats (1-11) of importin b bound to the non-classical NLS(67-94) of PTHrP | ||||||
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![]() | PROTEIN TRANSPORT / all helical protein / HEAT repeats | ||||||
Function / homology | ![]() negative regulation of chondrocyte development / regulation of chondrocyte differentiation / RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / establishment of mitotic spindle localization / astral microtubule organization / cAMP metabolic process / Transport of Ribonucleoproteins into the Host Nucleus ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / establishment of mitotic spindle localization / astral microtubule organization / cAMP metabolic process / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Nuclear import of Rev protein / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / Postmitotic nuclear pore complex (NPC) reformation / osteoblast development / peptide hormone receptor binding / nuclear import signal receptor activity / nuclear localization sequence binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / bone mineralization / mitotic spindle assembly / epidermis development / nuclear pore / Assembly of the ORC complex at the origin of replication / skeletal system development / female pregnancy / Hsp90 protein binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / specific granule lumen / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / cell-cell signaling / nuclear envelope / G alpha (s) signalling events / regulation of gene expression / nuclear membrane / ficolin-1-rich granule lumen / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / Golgi apparatus / enzyme binding / RNA binding / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cingolani, G. / Bednenko, J. / Gillespie, M.T. / Gerace, L. | ||||||
![]() | ![]() Title: Molecular basis for the recognition of a nonclassical nuclear localization signal by importin beta Authors: Cingolani, G. / Bednenko, J. / Gillespie, M.T. / Gerace, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 374.6 KB | Display | ![]() |
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Full document | ![]() | 417 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qgkS S: Starting model for refinement |
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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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Details | There is one biological assembly [importin b(1-485):PTHrP(67-94)] per asymmetryc unit |
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Components
#1: Protein | Mass: 53899.285 Da / Num. of mol.: 1 / Fragment: N-terminal domain (Residues 1-485) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3270.812 Da / Num. of mol.: 1 / Fragment: Residues 67-94 / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN). References: UniProt: P12272 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 6 Details: MES, PEG 4000, sodium chloride, Tween, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Conti, E., (1998) Cell, 94, 193. | ||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 16459 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 18.03 % / Biso Wilson estimate: 67.9 Å2 / Rmerge(I) obs: 0.0116 / Rsym value: 0.0116 / Net I/σ(I): 17.32 |
Reflection shell | Highest resolution: 2.9 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.469 / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Num. measured all: 296796 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 99.3 % / Rmerge(I) obs: 0.469 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QGK Resolution: 2.9→50 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å /
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.009 |