+Open data
-Basic information
Entry | Database: PDB / ID: 1o6p | ||||||
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Title | Importin Beta bound to a GLFG Nucleoporin peptide | ||||||
Components |
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Keywords | NUCLEAR TRANSPORT / NUCLEAR TRAFFICKING / NUCLEOPORIN / TRANSPORT FACTOR / PROTEIN TRANSPORT | ||||||
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 / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus ...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 / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / SUMOylation of SUMOylation proteins / 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 / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / Nuclear import of Rev protein / RNA export from nucleus / SUMOylation of chromatin organization proteins / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / mitotic spindle assembly / ribosomal large subunit export from nucleus / mRNA export from nucleus / 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 / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / ATPase binding / 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 / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Bayliss, R. / Stewart, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Glfg and Fxfg Nucleoporins Bind to Overlapping Sites on Importin-Beta Authors: Bayliss, R. / Littlewood, T. / Strawn, L.A. / Wente, S.R. / Stewart, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o6p.cif.gz | 179.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o6p.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 1o6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o6p_validation.pdf.gz | 391.4 KB | Display | wwPDB validaton report |
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Full document | 1o6p_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | 1o6p_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 1o6p_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/1o6p ftp://data.pdbj.org/pub/pdb/validation_reports/o6/1o6p | HTTPS FTP |
-Related structure data
Related structure data | 1o6oC 1qgrS 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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Details | A TRIMERIC ASSEMBLY IS FORMED BY THE ASSOCIATIONOF TWO MOLECULES OF THE PEPTIDE BOUND TO ONE MOLECULEOF CHAINS A AND B |
-Components
#1: Protein | Mass: 49385.203 Da / Num. of mol.: 2 / Fragment: IMPORTIN BETA-1 SUBUNIT, RESIDUES 1-442 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q14974 #2: Protein/peptide | Mass: 867.925 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: UniProt: Q02630*PLUS #3: Water | ChemComp-HOH / | |
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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: 5.27 Å3/Da / Density % sol: 77.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 100MM AMMONIUM ACETATE PH6.0, 1.2M AMMONIUM SULPHATE, pH 6.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→67.4 Å / Num. obs: 48209 / % possible obs: 91.8 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.9 |
Reflection | *PLUS Num. measured all: 257406 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 89.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QGR Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.269 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |