+Open data
-Basic information
Entry | Database: PDB / ID: 1wwh | ||||||
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Title | Crystal structure of the MPPN domain of mouse Nup35 | ||||||
Components | nucleoporin 35 | ||||||
Keywords | PROTEIN TRANSPORT / Structural Genomics / MPPN / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / nuclear pore central transport channel / nuclear pore organization / nuclear lamina / nuclear pore nuclear basket / structural constituent of nuclear pore / NLS-bearing protein import into nucleus / mRNA transport / cellular response to leukemia inhibitory factor / phospholipid binding / single-stranded DNA binding / nuclear membrane / regulation of DNA-templated transcription / nucleoplasm / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Handa, N. / Murayama, K. / Kukimoto, M. / Hamana, H. / Uchikubo, T. / Takemoto, C. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: The crystal structure of mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain Authors: Handa, N. / Kukimoto-Niino, M. / Akasaka, R. / Kishishita, S. / Murayama, K. / Terada, T. / Inoue, M. / Kigawa, T. / Kose, S. / Imamoto, N. / Tanaka, A. / Hayashizaki, Y. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wwh.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wwh.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/1wwh ftp://data.pdbj.org/pub/pdb/validation_reports/ww/1wwh | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12905.403 Da / Num. of mol.: 4 / Fragment: RRM-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / References: UniProt: Q9D7J2, UniProt: Q8R4R6*PLUS #2: 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: 3.3 Å3/Da / Density % sol: 62.5 % / Description: The file contains Friedel pairs. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9791, 0.9794, 0.9640 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 6, 2004 | ||||||||||||
Radiation | Monochromator: Si III / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. obs: 34813 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 62.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 14.5 | ||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.307 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→19.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 154018.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: The file contains Friedel pairs.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.942 Å2 / ksol: 0.344438 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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