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Yorodumi- PDB-1un0: Crystal Structure of Yeast Karyopherin (Importin) alpha in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1un0 | ||||||
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Title | Crystal Structure of Yeast Karyopherin (Importin) alpha in complex with a Nup2p N-terminal fragment | ||||||
Components |
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Keywords | NUCLEAR IMPORT / ARMADILLO REPEAT / NUCLEOPORIN / NLS RELEASE / KARYOPHERIN RECYCLING | ||||||
Function / homology | Function and homology information proteasome localization / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / import into nucleus / 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 / nuclear pore nuclear basket ...proteasome localization / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / import into nucleus / 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 / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / protein targeting to membrane / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / subtelomeric heterochromatin formation / nuclear pore / protein export from nucleus / GTPase activator activity / small GTPase binding / protein import into nucleus / disordered domain specific binding / nuclear envelope / nuclear membrane / chromosome, telomeric region / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Matsuura, Y. / Lange, A. / Harreman, M.T. / Corbett, A.H. / Stewart, M. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Structural Basis for Nup2P Function in Cargo Release and Karyopherin Recycling in Nuclear Import Authors: Matsuura, Y. / Lange, A. / Harreman, M.T. / Corbett, A.H. / Stewart, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1un0.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1un0.ent.gz | 149.7 KB | Display | PDB format |
PDBx/mmJSON format | 1un0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1un0_validation.pdf.gz | 391.4 KB | Display | wwPDB validaton report |
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Full document | 1un0_full_validation.pdf.gz | 415.2 KB | Display | |
Data in XML | 1un0_validation.xml.gz | 21 KB | Display | |
Data in CIF | 1un0_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/1un0 ftp://data.pdbj.org/pub/pdb/validation_reports/un/1un0 | HTTPS FTP |
-Related structure data
Related structure data | 1ee4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48906.562 Da / Num. of mol.: 2 / Fragment: ARMADILLO REPEAT DOMAIN, RESIDUES 88-530 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02821 #2: Protein | Mass: 5813.649 Da / Num. of mol.: 2 / Fragment: N-TERMINAL FRAGMENT, RESIDUES 1-51 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32499 #3: Water | ChemComp-HOH / | Compound details | CHAIN A, B ENGINEERED | |
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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: 2.4 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: 50 MM HEPES PH 6.8, 0.15 M NACL, 24 % PEG3350, 2 % PEG400 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6.8 / 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: PX14.2 / Wavelength: 0.978 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 21, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 29670 / % possible obs: 97.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. measured all: 76810 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 98.3 % / Num. unique obs: 4308 / Num. measured obs: 10875 / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EE4 Resolution: 2.6→20 Å / SU B: 11.435 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.686 / ESU R Free: 0.316
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Displacement parameters | Biso mean: 49.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.216 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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