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- PDB-8kcq: Solution structures of the N-terminal divergent caplonin homology... -

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Basic information

Entry
Database: PDB / ID: 8kcq
TitleSolution structures of the N-terminal divergent caplonin homology (NN-CH) domains of human intraflagellar transport protein 54
ComponentsTRAF3-interacting protein 1
KeywordsTRANSPORT PROTEIN / NN-CH domain / Intraflagellar transport (IFT) machinery / IFT54 / ciliopathy / Structural Genomics / PSI-2 / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


intraciliary anterograde transport / intraciliary transport particle B / negative regulation of defense response to virus / intraciliary transport / ciliary transition zone / ciliary tip / morphogenesis of a polarized epithelium / Intraflagellar transport / negative regulation of type I interferon production / ciliary base ...intraciliary anterograde transport / intraciliary transport particle B / negative regulation of defense response to virus / intraciliary transport / ciliary transition zone / ciliary tip / morphogenesis of a polarized epithelium / Intraflagellar transport / negative regulation of type I interferon production / ciliary base / axoneme / cilium assembly / negative regulation of protein-containing complex assembly / regulation of microtubule cytoskeleton organization / ciliary basal body / negative regulation of protein phosphorylation / kidney development / cilium / microtubule binding / centrosome
Similarity search - Function
TRAF3-interacting protein 1, N-terminal / TRAF3-interacting protein 1, C-terminal domain / TRAF3-interacting protein 1, N-terminal domain superfamily / Microtubule-binding protein MIP-T3 CH-like domain / Microtubule-binding protein MIP-T3 C-terminal region / TRAF3-interacting protein 1
Similarity search - Domain/homology
TRAF3-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / sumilated annealing
AuthorsDang, W. / Kuwasako, K. / He, F. / Takahashi, M. / Tsuda, K. / Nagata, T. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guentert, P. ...Dang, W. / Kuwasako, K. / He, F. / Takahashi, M. / Tsuda, K. / Nagata, T. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guentert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomol.Nmr Assign. / Year: 2024
Title: 1 H, 13 C, and 15 N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54.
Authors: Kuwasako, K. / Dang, W. / He, F. / Takahashi, M. / Tsuda, K. / Nagata, T. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guntert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y.
History
DepositionAug 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAF3-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)15,4011
Polymers15,4011
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TRAF3-interacting protein 1


Mass: 15401.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF3IP1 / Details (production host): CELL-Free Protein Synthesis
Production host: Cell-free gateway cloning vector N-term 8xHis mcherry pCellFree_G05 (others)
References: UniProt: Q8TDR0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 13C,15N-SEPARATED NOESY SPECTRA
121isotropic23D CBCA(CO)NH
131isotropic23D HN(CA)CB
141isotropic23D (H)CCH-COSY
151isotropic23D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-99% 13C; U-99% 15N] NN-CH domain of human IFT54, 100 mM None NaCl, 1 mM [U-99% 2H] d-DTT, 20 mM [U-99% 2H] d-Tris HCl, 0.02 % None NaN3, 90% H2O/10% D2O
Details: 1mM D-DTT;0.02% NaN3 were used to keep the protein condition
Label: 13C,15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMNN-CH domain of human IFT54[U-99% 13C; U-99% 15N]1
100 mMNaClNone1
1 mMd-DTT[U-99% 2H]1
20 mMd-Tris HCl[U-99% 2H]1
0.02 %NaN3None1
Sample conditionsDetails: 20mM D-Tris-HCL (PH7.0); 100mM NaCl; 1mM D-DTT;0.02% NaN3
Ionic strength: 100 mM / Label: condition_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE80013D_13C,15N-SEPARATED_NOESY
Bruker AVANCEBrukerAVANCE6002Assignments (CBCACONH et al.)

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Processing

NMR software
NameVersionDeveloperClassification
KUJIRA0.863N. Kobayashi, T. Kigawa, S. Yokoyamachemical shift assignment
CYANA2.2Guntert, Mumenthaler and Wuthrichstructure calculation
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
MagRO-NMRView1.2.38N. Kobayashipeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
TopSpinBruker Biospinprocessing
RefinementMethod: sumilated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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