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Yorodumi- PDB-2q5d: Crystal Structure of Human Importin Beta bound to the Snurportin1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q5d | ||||||
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Title | Crystal Structure of Human Importin Beta bound to the Snurportin1 IBB-domain second crystal form | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / HEAT REPEAT / IBB-DOMAIN / IMPORTIN / KARYOPHERIN / SNURPORTIN | ||||||
Function / homology | Function and homology information 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 / RNA cap binding / snRNA import into nucleus / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) ...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 / RNA cap binding / snRNA import into nucleus / 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 / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / 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 / specific granule lumen / protein import into nucleus / nuclear envelope / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / snRNP Assembly / nuclear membrane / ficolin-1-rich granule lumen / protein domain specific binding / Neutrophil degranulation / enzyme binding / RNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Mitrousis, G. / Cingolani, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Molecular Basis for the Recognition of Snurportin 1 by Importin {beta}. Authors: Mitrousis, G. / Olia, A.S. / Walker-Kopp, N. / Cingolani, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q5d.cif.gz | 345.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q5d.ent.gz | 280.5 KB | Display | PDB format |
PDBx/mmJSON format | 2q5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q5d_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 2q5d_full_validation.pdf.gz | 570.5 KB | Display | |
Data in XML | 2q5d_validation.xml.gz | 73.2 KB | Display | |
Data in CIF | 2q5d_validation.cif.gz | 96.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/2q5d ftp://data.pdbj.org/pub/pdb/validation_reports/q5/2q5d | HTTPS FTP |
-Related structure data
Related structure data | 2p8qC 1qgkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 97257.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB1, NTF97 / Plasmid: PQE-3 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q14974 #2: Protein/peptide | Mass: 5027.755 Da / Num. of mol.: 2 / Fragment: N-terminal domain (25-64) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O95149 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.69 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 22%PEG 8000, 0.05M SODIUM CHLORIDE 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→40 Å / Num. all: 50424 / Num. obs: 50424 / % possible obs: 78.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 66.8 Å2 |
Reflection shell | Resolution: 3.2→3.31 Å / Mean I/σ(I) obs: 1.72 / Num. unique all: 1763 / % possible all: 51.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qgk Resolution: 3.2→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 66 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.22 Å /
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