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- PDB-4nfm: Human tau tubulin kinase 1 (TTBK1) -

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Basic information

Entry
Database: PDB / ID: 4nfm
TitleHuman tau tubulin kinase 1 (TTBK1)
ComponentsTau-tubulin kinase 1
KeywordsTRANSFERASE / protein kinase / phosphotransferase
Function / homology
Function and homology information


positive regulation of astrocyte activation / positive regulation of microglial cell activation / microtubule associated complex / tau-protein kinase activity / positive regulation of protein polymerization / substantia nigra development / peptidyl-threonine phosphorylation / peptidyl-tyrosine phosphorylation / tau protein binding / peptidyl-serine phosphorylation ...positive regulation of astrocyte activation / positive regulation of microglial cell activation / microtubule associated complex / tau-protein kinase activity / positive regulation of protein polymerization / substantia nigra development / peptidyl-threonine phosphorylation / peptidyl-tyrosine phosphorylation / tau protein binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / learning or memory / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tau-tubulin kinase 1, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Tau-tubulin kinase 1, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tau-tubulin kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsSheriff, S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: The structure of human tau-tubulin kinase 1 both in the apo form and in complex with an inhibitor.
Authors: Kiefer, S.E. / Chang, C.J. / Kimura, S.R. / Gao, M. / Xie, D. / Zhang, Y. / Zhang, G. / Gill, M.B. / Mastalerz, H. / Thompson, L.A. / Cacace, A.M. / Sheriff, S.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Data collection
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tau-tubulin kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9762
Polymers37,8841
Non-polymers921
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.300, 39.900, 50.400
Angle α, β, γ (deg.)90.000, 104.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tau-tubulin kinase 1 / Brain-derived tau kinase


Mass: 37883.574 Da / Num. of mol.: 1 / Fragment: Kinase domain (UNP residues 13-343)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTBK1, BDTK, KIAA1855 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9
References: UniProt: Q5TCY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Ammonium Acetate, pH 7.0, 19% (w/v) PEG5000 (methyl ester), 100 mM Ammonium Acetate, unbuffered, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9797 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 18769 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 48.27 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.3
Reflection shellResolution: 2.12→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.11data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
AMoREphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CKI

1cki


Resolution: 2.12→47.48 Å / Cor.coef. Fo:Fc: 0.9526 / Cor.coef. Fo:Fc free: 0.9378 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1002 5.34 %RANDOM
Rwork0.2038 ---
obs0.2058 18767 98.92 %-
Displacement parametersBiso max: 123.66 Å2 / Biso mean: 53.5032 Å2 / Biso min: 28.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.0777 Å20 Å23.1937 Å2
2---2.2581 Å20 Å2
3---3.3358 Å2
Refine analyzeLuzzati coordinate error obs: 0.292 Å
Refinement stepCycle: LAST / Resolution: 2.12→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 6 80 2377
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d812SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes348HARMONIC5
X-RAY DIFFRACTIONt_it2348HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion293SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2728SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2348HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3171HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion17.75
LS refinement shellResolution: 2.12→2.25 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3217 159 5.42 %
Rwork0.2515 2773 -
all0.2552 2932 -
obs--98.92 %

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