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Yorodumi- PDB-1qgr: STRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN AL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qgr | ||||||
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Title | STRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN ALPHA (II CRYSTAL FORM, GROWN AT LOW PH) | ||||||
Components |
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Keywords | TRANSPORT RECEPTOR / NUCLEAR IMPORT / HEAT MOTIF / NLS-BINDING | ||||||
Function / homology | Function and homology information RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / Sensing of DNA Double Strand Breaks / endoplasmic reticulum tubular network / regulation of DNA recombination / establishment of mitotic spindle localization / astral microtubule organization / entry of viral genome into host nucleus through nuclear pore complex via importin / Transport of Ribonucleoproteins into the Host Nucleus ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / Sensing of DNA Double Strand Breaks / endoplasmic reticulum tubular network / regulation of DNA recombination / establishment of mitotic spindle localization / astral microtubule organization / entry of viral genome into host nucleus through nuclear pore complex via importin / Transport of Ribonucleoproteins into the Host Nucleus / positive regulation of viral life cycle / Regulation of cholesterol biosynthesis by SREBP (SREBF) / ribosomal protein import into nucleus / importin-alpha family protein binding / NS1 Mediated Effects on Host Pathways / Initiation of Nuclear Envelope (NE) Reformation / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / host cell / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear localization sequence binding / DNA metabolic process / CaMK IV-mediated phosphorylation of CREB / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / mitotic spindle assembly / nuclear pore / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / specific granule lumen / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / nuclear membrane / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / protein domain specific binding / Golgi membrane / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cingolani, G. / Petosa, C. / Weis, K. / Muller, C.W. | ||||||
Citation | Journal: Nature / Year: 1999 Title: Structure of importin-beta bound to the IBB domain of importin-alpha. Authors: Cingolani, G. / Petosa, C. / Weis, K. / Muller, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qgr.cif.gz | 185.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qgr.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/1qgr ftp://data.pdbj.org/pub/pdb/validation_reports/qg/1qgr | HTTPS FTP |
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-Related structure data
Related structure data | 1qgkSC 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 | Mass: 97323.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PEQ60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q14974 |
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#2: Protein/peptide | Mass: 3406.046 Da / Num. of mol.: 1 / Fragment: IBB DOMAIN / Source method: obtained synthetically Details: THIS PROTEIN IS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF HOMO SAPIENS (HUMAN). References: UniProt: P52292 |
#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: 2.43 Å3/Da / Density % sol: 48.1 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.9 / Details: pH 3.9 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-3 / Wavelength: 0.997 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 46295 / % possible obs: 98.5 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.3→2.37 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / Rsym value: 0.38 / % possible all: 98.5 |
Reflection shell | *PLUS % possible obs: 98.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB IDCODE 1QGK Resolution: 2.3→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / Rfactor obs: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |