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- PDB-1s1n: SH3 domain of human nephrocystin -

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Basic information

Entry
Database: PDB / ID: 1s1n
TitleSH3 domain of human nephrocystin
ComponentsNephrocystin 1
KeywordsCELL 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 / cilium / cell-cell adhesion / cell-cell junction / retina development in camera-type eye / actin cytoskeleton organization / cytoskeleton / structural molecule activity / signal transduction / membrane / cytosol / cytoplasm
Similarity search - Function
Nephrocystin-1, SH3 domain / Nephrocystin-1 / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry follwed by restrained simulated annealing
AuthorsLe 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
DepositionJan 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation_author.name
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nephrocystin 1


Theoretical massNumber of molelcules
Total (without water)7,6231
Polymers7,6231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 20structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average,lowest energy

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Components

#1: Protein Nephrocystin 1 / Juvenile nephronophthisis 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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
141HNHB
1512D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 1.5 mM SH3 domain U-15N,13C; 20mM phosphate buffer K, pH6.5
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM K-phosphate / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DIANA2.8Guentertstructure solution
X-PLOR3.89Brungerrefinement
RefinementMethod: 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 representativeSelection criteria: closest to the average,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 17

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