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- PDB-9f4c: Structure of the C-terminal domain of CKAP5/chTOG -

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Basic information

Entry
Database: PDB / ID: 9f4c
TitleStructure of the C-terminal domain of CKAP5/chTOG
ComponentsCytoskeleton-associated protein 5
KeywordsCELL CYCLE / microtubule / TACC3 binding
Function / homology
Function and homology information


microtubule plus end polymerase / establishment or maintenance of microtubule cytoskeleton polarity / RNA transport / positive regulation of microtubule nucleation / microtubule plus-end binding / centrosome cycle / microtubule depolymerization / spindle organization / microtubule polymerization / centrosome duplication ...microtubule plus end polymerase / establishment or maintenance of microtubule cytoskeleton polarity / RNA transport / positive regulation of microtubule nucleation / microtubule plus-end binding / centrosome cycle / microtubule depolymerization / spindle organization / microtubule polymerization / centrosome duplication / ribonucleoprotein complex binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / 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 / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / mitotic spindle organization / RHO GTPases Activate Formins / kinetochore / spindle pole / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / microtubule binding / ciliary basal body / cilium / cadherin binding / cell division / centrosome / nucleolus / protein-containing complex / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
XMAP215 family / CLASP N-terminal domain / CLASP N terminal / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Cytoskeleton-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPfuhl, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: J.Cell Biol. / Year: 2025
Title: Structure and dynamics of the C-terminus of CKAP5
Authors: Burgess, S.G. / Bayliss, R. / Pfuhl, M. / Rostkova, L. / Royle, S.
History
DepositionApr 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoskeleton-associated protein 5


Theoretical massNumber of molelcules
Total (without water)15,8841
Polymers15,8841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytoskeleton-associated protein 5 / Colonic and hepatic tumor overexpressed gene protein / Ch-TOG


Mass: 15883.864 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues G1815-P1958 / Source: (gene. exp.) Homo sapiens (human) / Gene: CKAP5, KIAA0097 / Plasmid: pETM6T / Details (production host): NusA fusion / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21* / References: UniProt: Q14008
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic33D 1H-15N NOESY
122isotropic13D 1H-13C NOESY aliphatic
132isotropic23D 1H-13C NOESY aromatic
141anisotropic115N IPAP
151isotropic12D 1H-15N HSQC
162isotropic12D 1H-13C HSQC aliphatic
172isotropic22D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-15N] CKAP5, 20 mM NA HEPES, 150 mM NA glutamic acid, 150 mM NA arginine, 2 mM NA DTT, 0.02 % NA NaN3, 95% H2O/5% D2Olabelled with 15N 20mM HEPES15N Sample95% H2O/5% D2O
solution20.5 mM [U-13C; U-15N] CKAP5, 20 mM NA HEPES, 150 mM NA glutamic acid, 150 mM NA arginine, 2 mM NA DTT, 0.02 % NA sodium azide, 95% H2O/5% D2Olabelled with 15N & 13C15N/13C Sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCKAP5[U-15N]1
20 mMHEPESNA1
150 mMglutamic acidNA1
150 mMarginineNA1
2 mMDTTNA1
0.02 %NaN3NA1
0.5 mMCKAP5[U-13C; U-15N]2
20 mMHEPESNA2
150 mMglutamic acidNA2
150 mMarginineNA2
2 mMDTTNA2
0.02 %sodium azideNA2
Sample conditionsIonic strength: 150 mM / Ionic strength err: 1 / Label: cond1 / pH: 7.2 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.05 / Temperature: 298 K / Temperature err: 0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III8001KCL
Bruker AVANCEBrukerAVANCE7002KCL
Bruker AVANCE III HDBrukerAVANCE III HD9503Crick

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.1Bruker Biospincollection
CcpNmr Analysis2.4CCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4 / Details: standard protocol
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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