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- PDB-7nwj: Solution NMR structure of the N-terminal domain of CEP164 (1-109) -

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Basic information

Entry
Database: PDB / ID: 7nwj
TitleSolution NMR structure of the N-terminal domain of CEP164 (1-109)
ComponentsCentrosomal protein of 164 kDa
KeywordsPROTEIN BINDING / centriolar protein / TTBK2 binding / ciliopathies
Function / homology
Function and homology information


ciliary transition fiber / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition ...ciliary transition fiber / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / cell cycle / cell division / intracellular membrane-bounded organelle / DNA repair / centrosome / extracellular space / nucleoplasm / cytosol
Similarity search - Function
WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Centrosomal protein of 164 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Authorsvan Breugel, M. / Rutherford, T.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/3 United Kingdom
CitationJournal: Structure / Year: 2022
Title: Molecular mechanisms underlying the role of the centriolar CEP164-TTBK2 complex in ciliopathies.
Authors: Rosa E Silva, I. / Bino, L. / Johnson, C.M. / Rutherford, T.J. / Neuhaus, D. / Andreeva, A. / Cajanek, L. / van Breugel, M.
History
DepositionMar 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed ..._citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Dec 21, 2022Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centrosomal protein of 164 kDa


Theoretical massNumber of molelcules
Total (without water)12,9511
Polymers12,9511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, monomeric by 1H spin-echo (1H T2)
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8750 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Centrosomal protein of 164 kDa / Cep164


Mass: 12950.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP164, KIAA1052, NPHP15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9UPV0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N BEST-TROSY
121isotropic32D 1H-13C HSQC aliphatic
131isotropic23D HN(CA)CO
141isotropic23D HN(CA)CB
152isotropic32D 1H-1H NOESY
161isotropic12D (HB)CB(CGCD)HD

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1120 uM [U-10% 13C; U-100% 15N] CEP164 (1-109), 25 mM sodium phosphate, 125 mM sodium chloride, 4 mM DTT, 0.4 % complete protease inhibotor cocktail, EDTA free, 95% H2O/5% D2O13C-15N sample95% H2O/5% D2O
solution2500 uM [U-10% 13C; U-100% 15N] CEP164 (1-109), 25 mM sodium phosphate, 125 mM sodium chloride, 4 mM DTT, 0.4 % complete protease inhibotor cocktail, EDTA free, 95% H2O/5% D2O15N sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
120 uMCEP164 (1-109)[U-10% 13C; U-100% 15N]1
25 mMsodium phosphatenatural abundance1
125 mMsodium chloridenatural abundance1
4 mMDTTnatural abundance1
0.4 %complete protease inhibotor cocktail, EDTA freenatural abundance1
500 uMCEP164 (1-109)[U-10% 13C; U-100% 15N]2
25 mMsodium phosphatenatural abundance2
125 mMsodium chloridenatural abundance2
4 mMDTTnatural abundance2
0.4 %complete protease inhibotor cocktail, EDTA freenatural abundance2
Sample conditionsIonic strength: 185 mM / Label: assignment / pH: 7.4 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001TCI cryoprobe
Bruker AVANCE IIBrukerAVANCE II7002TCI cryoprobe
Bruker AVANCE III HDBrukerAVANCE III HD8003TCI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
NMRFAM-SPARKY1.3NMRFAMchemical shift assignment
X-PLOR NIH2.28Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Amber11Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
TALOS+3.80F1 Rev 2012.080.14.41Shen, Delaglio, Cormilescu and Baxdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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