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Yorodumi- PDB-6wba: Structure of Mouse Importin alpha MLH1- R470A NLS Peptide Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wba | |||||||||
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Title | Structure of Mouse Importin alpha MLH1- R470A NLS Peptide Complex | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT/NUCLEAR PROTEIN / Importin alpha / Nuclear Import / NLS / MLH1 / PROTEIN TRANSPORT / PROTEIN TRANSPORT-NUCLEAR PROTEIN complex | |||||||||
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 / MutLalpha complex / meiotic spindle midzone assembly / 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 / MutLalpha complex / meiotic spindle midzone assembly / 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 / synaptonemal complex / entry of viral genome into host nucleus through nuclear pore complex via importin / female meiosis chromosome segregation / positive regulation of viral life cycle / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / ATP-dependent DNA damage sensor activity / nuclear localization sequence binding / oogenesis / NLS-bearing protein import into nucleus / somatic hypermutation of immunoglobulin genes / mismatch repair / host cell / male germ cell nucleus / TP53 Regulates Transcription of DNA Repair Genes / response to bacterium / Meiotic recombination / cytoplasmic stress granule / double-strand break repair via nonhomologous end joining / protein import into nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / 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 / MOLECULAR REPLACEMENT / Resolution: 2.151 Å | |||||||||
Authors | de Barros, A.C. / da Silva, T.D. / Oliveira, H.C. / Fukuda, C.A. / Fontes, M.R.M. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Biochem.J. / Year: 2021 Title: Structural and calorimetric studies reveal specific determinants for the binding of a high-affinity NLS to mammalian importin-alpha. Authors: de Oliveira, H.C. / da Silva, T.D. / Salvador, G.H.M. / Moraes, I.R. / Fukuda, C.A. / de Barros, A.C. / 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 | 6wba.cif.gz | 191.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wba.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/6wba ftp://data.pdbj.org/pub/pdb/validation_reports/wb/6wba | HTTPS FTP |
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-Related structure data
Related structure data | 6wbbC 6wbcC 7m60C 5u5pS 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: 49886.633 Da / Num. of mol.: 1 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 | ||
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#2: Protein/peptide | Mass: 1300.382 Da / Num. of mol.: 2 / Fragment: NLS peptide / Mutation: R470A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40692 #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M sodium citrate (pH 6), 0.6 M sodium citrate and 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.425 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→43.524 Å / Num. obs: 508565 / % possible obs: 98.95 % / Redundancy: 13.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09852 / Rpim(I) all: 0.02786 / Rrim(I) all: 0.1025 / Net I/σ(I): 23.22 |
Reflection shell | Resolution: 2.151→2.228 Å / Rmerge(I) obs: 1.327 / Mean I/σ(I) obs: 2 / Num. unique obs: 3719 / CC1/2: 0.803 / Rpim(I) all: 0.3732 / Rrim(I) all: 1.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5u5p Resolution: 2.151→43.524 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.18 Å2 / Biso mean: 52.0085 Å2 / Biso min: 24.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.151→43.524 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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