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- PDB-6o1q: The N-terminal domain of NPHP1 folds into an antiparallel three-s... -

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Basic information

Entry
Database: PDB / ID: 6o1q
TitleThe N-terminal domain of NPHP1 folds into an antiparallel three-stranded coiled coil
ComponentsNephrocystin-1
KeywordsAPOPTOSIS / nephronophthisis
Function / homology
Function and homology information


protein localization involved in establishment of planar polarity / spermatid differentiation / visual behavior / photoreceptor connecting cilium / cell projection organization / positive regulation of bicellular tight junction assembly / motile cilium / bicellular tight junction / Anchoring of the basal body to the plasma membrane / adherens junction ...protein localization involved in establishment of planar polarity / spermatid differentiation / visual behavior / photoreceptor connecting cilium / cell projection organization / positive regulation of bicellular tight junction assembly / motile cilium / bicellular tight junction / Anchoring of the basal body to the plasma membrane / adherens junction / cell-cell adhesion / cell-cell junction / actin cytoskeleton organization / retina development in camera-type eye / cytoskeleton / cilium / structural molecule activity / signal transduction / membrane / cytosol / cytoplasm
Similarity search - Function
Nephrocystin-1, SH3 domain / Nephrocystin-1 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMusco, G. / Mannella, V.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione CARIPLOR0532 Italy
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: The N-Terminal Domain of NPHP1 Folds into a Monomeric Left-Handed Antiparallel Three-Stranded Coiled Coil with Anti-apoptotic Function.
Authors: Mannella, V. / Quilici, G. / Nigro, E.A. / Lampis, M. / Minici, C. / Degano, M. / Boletta, A. / Musco, G.
History
DepositionFeb 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nephrocystin-1


Theoretical massNumber of molelcules
Total (without water)13,6761
Polymers13,6761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9110 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nephrocystin-1 / Juvenile nephronophthisis 1 protein


Mass: 13676.493 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPHP1, NPH1 / Production host: Escherichia coli (E. coli) / References: UniProt: O15259

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic12D 1H-1H NOESY
124isotropic12D 1H-1H TOCSY
135isotropic12D 1H-1H NOESY
145isotropic12D 1H-1H TOCSY
153isotropic12D 1H-15N HSQC
163isotropic13D HNHA
173isotropic23D 1H-15N NOESY
182isotropic13D HNCA
192isotropic13D H(CCO)NH
1102isotropic13D HN(CA)CB
1112isotropic13D CBCA(CO)NH
1122isotropic13D C(CO)NH
1132isotropic13D HNCO
1141isotropic23D (H)CCH-TOCSY
1151isotropic22D 1H-13C HSQC
1161isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 13C; U-99% 15N] NPHP1 CC, 100% D2O15N-13C_sample100% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] NPHP1CC, 90% H2O/10% D2O15N-13C_sample_290% H2O/10% D2O
solution30.9 mM [U-99% 15N] NPHP1CC, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution40.7 mM NPHP1CC, 90% H2O/10% D2Ounlab_sample90% H2O/10% D2O
solution50.7 mM NPHP1CC, 100% D2Ounlab_sample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMNPHP1 CC[U-99% 13C; U-99% 15N]1
0.8 mMNPHP1CC[U-99% 13C; U-99% 15N]2
0.9 mMNPHP1CC[U-99% 15N]3
0.7 mMNPHP1CCnatural abundance4
0.7 mMNPHP1CCnatural abundance5
Sample conditionsIonic strength: 0.15 M / Label: condition_15N-13C_sample / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
AnalysisCCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 10

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