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Yorodumi- PDB-4wv6: Heterodimer of Importin alpha 1 with nuclear localization signal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wv6 | ||||||
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Title | Heterodimer of Importin alpha 1 with nuclear localization signal of TAF8 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Nuclear import / Armadillo repeats / NLS | ||||||
Function / homology | Function and homology information Sensing of DNA Double Strand Breaks / regulation of DNA recombination / DNA-templated transcription open complex formation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / maintenance of protein location in nucleus / regulation of fat cell differentiation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...Sensing of DNA Double Strand Breaks / regulation of DNA recombination / DNA-templated transcription open complex formation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / maintenance of protein location in nucleus / regulation of fat cell differentiation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / inner cell mass cell proliferation / nuclear import signal receptor activity / DNA metabolic process / CaMK IV-mediated phosphorylation of CREB / nuclear localization sequence binding / NLS-bearing protein import into nucleus / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II transcribes snRNA genes / positive regulation of type I interferon production / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / mRNA transcription by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ISG15 antiviral mechanism / histone deacetylase binding / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / host cell / nuclear membrane / Estrogen-dependent gene expression / cell differentiation / protein heterodimerization activity / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Trowitzsch, S. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2015 Title: Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules. Authors: Trowitzsch, S. / Viola, C. / Scheer, E. / Conic, S. / Chavant, V. / Fournier, M. / Papai, G. / Ebong, I.O. / Schaffitzel, C. / Zou, J. / Haffke, M. / Rappsilber, J. / Robinson, C.V. / ...Authors: Trowitzsch, S. / Viola, C. / Scheer, E. / Conic, S. / Chavant, V. / Fournier, M. / Papai, G. / Ebong, I.O. / Schaffitzel, C. / Zou, J. / Haffke, M. / Rappsilber, J. / Robinson, C.V. / Schultz, P. / Tora, L. / Berger, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wv6.cif.gz | 271.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wv6.ent.gz | 221.4 KB | Display | PDB format |
PDBx/mmJSON format | 4wv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wv6_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 4wv6_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 4wv6_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 4wv6_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/4wv6 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/4wv6 | HTTPS FTP |
-Related structure data
Related structure data | 4wv4C 3rz9S 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: 50988.684 Da / Num. of mol.: 1 / Fragment: UNP residues 60-529 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52292 | ||||
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#2: Protein/peptide | Mass: 1672.133 Da / Num. of mol.: 2 / Fragment: UNP residues 297-310 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z7C8 #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.71 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: HEPES-NaOH, polyethylene glycole 3350, L-proline |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→49.54 Å / Num. obs: 55423 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.18 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.7745 / Mean I/σ(I) obs: 2.03 / Num. measured obs: 5436 / % possible all: 99.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RZ9 Resolution: 1.75→49.536 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→49.536 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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