+Open data
-Basic information
Entry | Database: PDB / ID: 1s1n | ||||||
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Title | SH3 domain of human nephrocystin | ||||||
Components | Nephrocystin 1 | ||||||
Keywords | CELL ADHESION / BETA BARREL | ||||||
Function / homology | Function and homology information protein localization involved in establishment of planar polarity / visual behavior / spermatid differentiation / photoreceptor connecting cilium / positive regulation of bicellular tight junction assembly / cell projection organization / motile cilium / bicellular tight junction / Anchoring of the basal body to the plasma membrane / adherens junction ...protein localization involved in establishment of planar polarity / visual behavior / spermatid differentiation / photoreceptor connecting cilium / positive regulation of bicellular tight junction assembly / cell projection organization / motile cilium / bicellular tight junction / Anchoring of the basal body to the plasma membrane / adherens junction / cell-cell adhesion / cilium / cell-cell junction / retina development in camera-type eye / actin cytoskeleton organization / cytoskeleton / structural molecule activity / signal transduction / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry follwed by restrained simulated annealing | ||||||
Authors | Le Maire, A. / Weber, T. / Saunier, S. / Antignac, C. / Ducruix, A. / Dardel, F. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Solution NMR structure of the SH3 domain of human nephrocystin and analysis of a mutation-causing juvenile nephronophthisis. Authors: le Maire, A. / Weber, T. / Saunier, S. / Broutin, I. / Antignac, C. / Ducruix, A. / Dardel, F. #1: Journal: HUM.MOL.GENET. / Year: 1997 Title: A novel gene that encodes a protein with a putative src homology 3 domain is a candidate gene for familial juvenile nephronophthisis Authors: SAUNIER, S. / CALADO, J. / HEILIG, R. / SILBERMANN, F. / BENESSY, F. / MORIN, G. / KONRAD, M. / BROYER, M. / GUBLER, M.C. / WEISSENBACH, J. #2: Journal: NAT.GENET. / Year: 1997 Title: A novel gene encoding an SH3 domain protein is mutated in nephronophthisis type 1 Authors: HILDEBRANDT, F. / OTTO, E. / RENSIG, C. / NOTHWANG, H.G. / VOLLMER, M. / ADOLPHS, J. / HANUSH, H. / BRANDIS, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s1n.cif.gz | 321.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s1n.ent.gz | 267.1 KB | Display | PDB format |
PDBx/mmJSON format | 1s1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s1n_validation.pdf.gz | 353.7 KB | Display | wwPDB validaton report |
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Full document | 1s1n_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 1s1n_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1s1n_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/1s1n ftp://data.pdbj.org/pub/pdb/validation_reports/s1/1s1n | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7623.472 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPHP1, NPH1 / Plasmid: PGEX-4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O15259 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details | Contents: 1.5 mM SH3 domain U-15N,13C; 20mM phosphate buffer K, pH6.5 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 20 mM K-phosphate / pH: 6.5 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry follwed by restrained simulated annealing Software ordinal: 1 Details: The structures are based on a total of 623 restraints. 540 are NOE-derived restraints : 110 intraresidue, 121 sequential, 37 medium-range and 272 long-range. 30 distance restraints from ...Details: The structures are based on a total of 623 restraints. 540 are NOE-derived restraints : 110 intraresidue, 121 sequential, 37 medium-range and 272 long-range. 30 distance restraints from hydrogen bonds. 53 dihedral angle restraints. | ||||||||||||
NMR representative | Selection criteria: closest to the average,lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 17 |