+Open data
-Basic information
Entry | Database: PDB / ID: 6iwa | ||||||
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Title | Crystal structure of Importin-alpha and phosphoserine GM130 | ||||||
Components |
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Keywords | PROTEIN BINDING / Importin alpha / GM130 | ||||||
Function / homology | Function and homology information meiotic spindle assembly / Golgi cis cisterna / positive regulation of protein glycosylation / Golgi disassembly / asymmetric cell division / Golgi ribbon formation / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / microtubule nucleation ...meiotic spindle assembly / Golgi cis cisterna / positive regulation of protein glycosylation / Golgi disassembly / asymmetric cell division / Golgi ribbon formation / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / microtubule nucleation / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / cis-Golgi network / postsynapse to nucleus signaling pathway / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / COPII-mediated vesicle transport / syntaxin binding / nuclear import signal receptor activity / nuclear localization sequence binding / Golgi cisterna membrane / NLS-bearing protein import into nucleus / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / protein glycosylation / COPII-coated ER to Golgi transport vesicle / Golgi organization / mitotic spindle assembly / spindle assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / negative regulation of autophagy / endoplasmic reticulum-Golgi intermediate compartment membrane / negative regulation of protein binding / mitotic spindle / spindle pole / cytoplasmic stress granule / protein import into nucleus / host cell / protein transport / microtubule binding / protein homotetramerization / DNA-binding transcription factor binding / microtubule / postsynaptic density / cadherin binding / Golgi membrane / glutamatergic synapse / protein kinase binding / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Chang, C.-C. / Chen, C.-J. / Pien, Y.-C. / Tsai, S.-Y. / Hsia, K.-C. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Ran pathway-independent regulation of mitotic Golgi disassembly by Importin-alpha. Authors: Chang, C.-C. / Chen, C.-J. / Grauffel, C. / Pien, Y.-C. / Lim, C. / Tsai, S.-Y. / Hsia, K.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iwa.cif.gz | 197.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iwa.ent.gz | 153.6 KB | Display | PDB format |
PDBx/mmJSON format | 6iwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iwa_validation.pdf.gz | 444.5 KB | Display | wwPDB validaton report |
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Full document | 6iwa_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 6iwa_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 6iwa_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/6iwa ftp://data.pdbj.org/pub/pdb/validation_reports/iw/6iwa | HTTPS FTP |
-Related structure data
Related structure data | 6iw8C 6k06C 1iq1S 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/peptide | Mass: 3315.868 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GOLGA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08379 |
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#2: Protein | Mass: 46898.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.82 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.1M Sodium citrate tribasic dihydrate, 16% w/v Polyethylene glycol 8000 (pH 5.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 28211 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rsym value: 0.042 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Num. unique obs: 2744 / CC1/2: 0.983 / Rsym value: 0.142 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IQ1 Resolution: 2.4→20 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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LS refinement shell | Highest resolution: 2.4 Å
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Refinement TLS params. | Method: refined / Origin x: -1.3191 Å / Origin y: 23.8423 Å / Origin z: 0.5434 Å
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Refinement TLS group | Selection details: ALL |