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- PDB-6vrf: ADP bound TTBK2 kinase domain -

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Basic information

Entry
Database: PDB / ID: 6vrf
TitleADP bound TTBK2 kinase domain
ComponentsTau-tubulin kinase 2
KeywordsTRANSFERASE / TTBK2 kinase domain
Function / homology
Function and homology information


negative regulation of protein localization to microtubule / cerebellar granular layer development / : / cerebellar granule cell precursor tangential migration / ciliary transition zone / negative regulation of microtubule depolymerization / microtubule plus-end binding / tau-protein kinase activity / smoothened signaling pathway / kinesin binding ...negative regulation of protein localization to microtubule / cerebellar granular layer development / : / cerebellar granule cell precursor tangential migration / ciliary transition zone / negative regulation of microtubule depolymerization / microtubule plus-end binding / tau-protein kinase activity / smoothened signaling pathway / kinesin binding / cilium assembly / centriole / cerebellum development / Anchoring of the basal body to the plasma membrane / regulation of cell migration / tau protein binding / microtubule cytoskeleton organization / peptidyl-serine phosphorylation / microtubule cytoskeleton / eukaryotic translation initiation factor 2alpha kinase activity / 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 / protein kinase activity / ciliary basal body / cilium / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / extracellular space / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / 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. ...: / : / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Tau-tubulin kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChodaparambil, J.V. / Marcotte, D.J.
CitationJournal: Cell Mol Neurobiol / Year: 2021
Title: Mechanisms of Regulation and Diverse Activities of Tau-Tubulin Kinase (TTBK) Isoforms.
Authors: Bao, C. / Bajrami, B. / Marcotte, D.J. / Chodaparambil, J.V. / Kerns, H.M. / Henderson, J. / Wei, R. / Gao, B. / Dillon, G.M.
History
DepositionFeb 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tau-tubulin kinase 2
B: Tau-tubulin kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,60819
Polymers68,7612
Non-polymers1,84717
Water16,214900
1
A: Tau-tubulin kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,20910
Polymers34,3811
Non-polymers8289
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tau-tubulin kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3999
Polymers34,3811
Non-polymers1,0188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.223, 114.625, 120.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tau-tubulin kinase 2


Mass: 34380.641 Da / Num. of mol.: 2 / Fragment: Kinase domain, residues 1-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTBK2, KIAA0847 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6IQ55, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 917 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 900 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M TRIS pH 8.5, 10% glycerol and 2.0M Na/K phosphate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 122628 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rsym value: 0.036 / Net I/σ(I): 7.6
Reflection shellResolution: 1.5→1.54 Å / Num. unique obs: 5774 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4btj

4btj


Resolution: 1.5→46.53 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.79
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 2010 1.64 %random
Rwork0.1742 ---
obs0.1748 122545 98.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4665 0 106 900 5671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164918
X-RAY DIFFRACTIONf_angle_d1.356638
X-RAY DIFFRACTIONf_dihedral_angle_d19.737700
X-RAY DIFFRACTIONf_chiral_restr0.088711
X-RAY DIFFRACTIONf_plane_restr0.01840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.37951430.34458305X-RAY DIFFRACTION96
1.54-1.580.2961330.27378476X-RAY DIFFRACTION98
1.58-1.630.27871430.23648476X-RAY DIFFRACTION98
1.63-1.680.2151380.20738535X-RAY DIFFRACTION98
1.68-1.740.21471500.19468553X-RAY DIFFRACTION98
1.74-1.810.21771470.18138541X-RAY DIFFRACTION98
1.81-1.890.24131420.18028572X-RAY DIFFRACTION99
1.89-1.990.1971350.18158626X-RAY DIFFRACTION99
1.99-2.110.2271440.16458378X-RAY DIFFRACTION96
2.11-2.280.20741470.16398689X-RAY DIFFRACTION99
2.28-2.510.20481450.16768731X-RAY DIFFRACTION100
2.51-2.870.2181430.17438802X-RAY DIFFRACTION100
2.87-3.610.19611500.16428863X-RAY DIFFRACTION100
3.62-46.530.18571500.1588988X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0985-2.1060.94962.4675-0.56991.816-0.2259-0.2939-0.12920.31020.24150.212-0.0784-0.2995-0.01270.16150.01270.02090.17350.00130.147-20.516417.55148.32
20.9324-0.0879-0.28992.1777-1.14411.58950.0040.0162-0.01820.0070.049-0.0070.0262-0.0835-0.0730.0895-0.0028-0.02880.1142-0.00030.1202-10.60835.0553-1.5255
31.42120.0598-0.00331.0840.15941.6510.0190.0643-0.16-0.12510.00270.01120.2305-0.0367-0.01830.1862-0.0072-0.02570.1468-0.00850.1818-8.8402-6.3969-6.8522
42.00550.08761.08151.6466-0.15642.2499-0.11050.11480.1073-0.0016-0.0439-0.2185-0.18730.18510.13120.13630.0037-0.01440.13830.01070.1494-21.110937.7357-13.7888
50.94620.18370.50981.2379-0.29641.76590.02910.0114-0.02260.0079-0.0438-0.0443-0.001-0.0559-0.00830.11440.0293-0.01130.14-0.00360.1306-31.139427.5826-26.2405
61.5774-0.402-0.34052.71480.98590.97540.02210.19310.0077-0.25540.0356-0.3517-0.0980.0892-0.04570.21440.02810.02510.2106-0.01630.1891-25.824124.3861-40.183
71.65490.38480.17772.1774-0.70322.05360.03010.1002-0.1645-0.0702-0.01240.10830.157-0.1258-0.00720.14310.016-0.01890.1937-0.02880.1685-40.140318.9451-34.5576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 95 )
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 298 )
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 94 )
5X-RAY DIFFRACTION5chain 'B' and (resid 95 through 186 )
6X-RAY DIFFRACTION6chain 'B' and (resid 187 through 241 )
7X-RAY DIFFRACTION7chain 'B' and (resid 242 through 298 )

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