+Open data
-Basic information
Entry | Database: PDB / ID: 7tmy | |||||||||
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Title | Structure of Mouse Importin alpha NEIL3 NLS Peptide Complex | |||||||||
Components |
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Keywords | NUCLEAR PROTEIN / Importin-alpha / Complex / BER / NLS | |||||||||
Function / homology | Function and homology information Defective Base Excision Repair Associated with NEIL3 / NEIL3-mediated resolution of ICLs / MCM complex binding / Sensing of DNA Double Strand Breaks / DNA N-glycosylase activity / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / bubble DNA binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway ...Defective Base Excision Repair Associated with NEIL3 / NEIL3-mediated resolution of ICLs / MCM complex binding / Sensing of DNA Double Strand Breaks / DNA N-glycosylase activity / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / bubble DNA binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / interstrand cross-link repair / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / cytoplasmic stress granule / protein import into nucleus / host cell / single-stranded DNA binding / double-stranded DNA binding / DNA-binding transcription factor binding / damaged DNA binding / postsynaptic density / glutamatergic synapse / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | |||||||||
Authors | Moraes, I.R. / de Oliveira, H.C. / Fontes, M.R.M. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2023 Title: Structural basis of nuclear transport for NEIL DNA glycosylases mediated by importin-alpha. Authors: Moraes, I.R. / de Oliveira, H.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 | 7tmy.cif.gz | 178.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tmy.ent.gz | 139.8 KB | Display | PDB format |
PDBx/mmJSON format | 7tmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tmy_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 7tmy_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 7tmy_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 7tmy_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/7tmy ftp://data.pdbj.org/pub/pdb/validation_reports/tm/7tmy | HTTPS FTP |
-Related structure data
Related structure data | 7tmxC 3ul1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 910.113 Da / Num. of mol.: 1 / Fragment: Residues 462-469 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q8TAT5, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase |
#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: 3.46 Å3/Da / Density % sol: 64.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: sodium citrate buffer (pH 6.0), sodium citrate and 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: 1.45 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→42.03 Å / Num. obs: 67874 / % possible obs: 99.62 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.183 / Net I/σ(I): 11.82 |
Reflection shell | Resolution: 2.21→2.29 Å / Redundancy: 12.7 % / Rmerge(I) obs: 2.53 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3511 / CC1/2: 0.8 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UL1 Resolution: 2.21→42.03 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.15 Å2 / Biso mean: 56.068 Å2 / Biso min: 26.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.21→42.03 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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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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