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Yorodumi- PDB-5u5p: Crystal Structure and X-ray Diffraction Data Collection of Import... -
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-Basic information
Entry | Database: PDB / ID: 5u5p | ||||||
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Title | Crystal Structure and X-ray Diffraction Data Collection of Importin-alpha from Mus Musculus Complexed with a MLH1 NLS Peptide | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Nuclear transport / Importin-alpha / MLH1 / NLS | ||||||
Function / homology | Function and homology information chiasma / late recombination nodule / male meiosis chromosome segregation / meiotic metaphase I homologous chromosome alignment / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / negative regulation of mitotic recombination / meiotic spindle midzone assembly / MutLalpha complex / guanine/thymine mispair binding ...chiasma / late recombination nodule / male meiosis chromosome segregation / meiotic metaphase I homologous chromosome alignment / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / negative regulation of mitotic recombination / meiotic spindle midzone assembly / MutLalpha complex / guanine/thymine mispair binding / meiotic telomere clustering / positive regulation of isotype switching to IgA isotypes / nuclear-transcribed mRNA poly(A) tail shortening / resolution of meiotic recombination intermediates / homologous chromosome pairing at meiosis / Sensing of DNA Double Strand Breaks / positive regulation of isotype switching to IgG isotypes / entry of viral genome into host nucleus through nuclear pore complex via importin / synaptonemal complex / female meiosis chromosome segregation / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / ATP-dependent DNA damage sensor activity / NLS-bearing protein import into nucleus / oogenesis / somatic hypermutation of immunoglobulin genes / mismatch repair / male germ cell nucleus / TP53 Regulates Transcription of DNA Repair Genes / response to bacterium / Meiotic recombination / double-strand break repair via nonhomologous end joining / cytoplasmic stress granule / protein import into nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / host cell / chromosome / spermatogenesis / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / chromatin binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.171 Å | ||||||
Authors | Barros, A.C. / Takeda, A.A. / Dreyer, T.R. / Velazquez-Campoy, A. / Kobe, B. / Fontes, M.R. | ||||||
Citation | Journal: Biochimie / Year: 2018 Title: DNA mismatch repair proteins MLH1 and PMS2 can be imported to the nucleus by a classical nuclear import pathway. Authors: de Barros, A.C. / Takeda, A.A.S. / Dreyer, T.R. / Velazquez-Campoy, A. / Kobe, B. / Fontes, M.R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u5p.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u5p.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 5u5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u5p_validation.pdf.gz | 469 KB | Display | wwPDB validaton report |
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Full document | 5u5p_full_validation.pdf.gz | 477.5 KB | Display | |
Data in XML | 5u5p_validation.xml.gz | 20 KB | Display | |
Data in CIF | 5u5p_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/5u5p ftp://data.pdbj.org/pub/pdb/validation_reports/u5/5u5p | HTTPS FTP |
-Related structure data
Related structure data | 5u5rC 1q1sS 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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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1299.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40692 #2: Protein | | Mass: 55330.566 Da / Num. of mol.: 1 / Fragment: residues 70-529 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: Chemical | ChemComp-DTT / | #4: 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: 2.95 Å3/Da / Density % sol: 58.28 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.600-0.625 M sodium citrate (pH 6) 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→40 Å / Num. obs: 36607 / % possible obs: 99.5 % / Redundancy: 6.4 % / Net I/σ(I): 24.11 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1Q1S Resolution: 2.171→38.579 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.171→38.579 Å
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Refine LS restraints |
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LS refinement shell |
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