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- PDB-6bdn: Crystal structure of human TAO3 kinase binding ADP -

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Basic information

Entry
Database: PDB / ID: 6bdn
TitleCrystal structure of human TAO3 kinase binding ADP
ComponentsSerine/threonine-protein kinase TAO3
KeywordsTRANSFERASE / TAOK3 / kinase / Serine/threonine-protein kinase / ADT-binding / MAPK cascade
Function / homology
Function and homology information


positive regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / protein kinase inhibitor activity / mitotic G2 DNA damage checkpoint signaling / regulation of MAPK cascade / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of JUN kinase activity / RAC1 GTPase cycle / neuron projection morphogenesis ...positive regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / protein kinase inhibitor activity / mitotic G2 DNA damage checkpoint signaling / regulation of MAPK cascade / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of JUN kinase activity / RAC1 GTPase cycle / neuron projection morphogenesis / positive regulation of JNK cascade / MAPK cascade / transferase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA damage response / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / Serine/threonine-protein kinase TAO3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAleshin, A.E. / Bankton, L.A. / Pinkerton, A. / Courtneidge, S.A. / Liddington, R.C.
CitationJournal: To Be Published
Title: Crystal structure of human TAO3 kinase binding ADP
Authors: Aleshin, A.E. / Bankton, L.A. / Pinkerton, A. / Liddington, R.C. / Courtneidge, S.A.
History
DepositionOct 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase TAO3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0435
Polymers36,4011
Non-polymers6434
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-31 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.187, 59.897, 110.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein kinase TAO3 / Cutaneous T-cell lymphoma-associated antigen HD-CL-09 / CTCL-associated antigen HD-CL-09 / ...Cutaneous T-cell lymphoma-associated antigen HD-CL-09 / CTCL-associated antigen HD-CL-09 / Dendritic cell-derived protein kinase / JNK/SAPK-inhibitory kinase / Jun kinase-inhibitory kinase / Kinase from chicken homolog A / hKFC-A / Thousand and one amino acid protein 3


Mass: 36400.738 Da / Num. of mol.: 1 / Fragment: UNP residues 1-316 / Mutation: R6A, K7A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAOK3, DPK, JIK, KDS, MAP3K18 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q9H2K8, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 250 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion, hanging drop
Details: Drops: 1.8 uL protein + 1.0 uL well solution, protein solution: 6.5 mg/mL TAO3K in 0.7 mM ADP, 5 mM magnesium chloride, 100 mM sodium chloride, 25 mM Tris, pH 8.0, 2 mM BME, 0.3 mM EDTA, ...Details: Drops: 1.8 uL protein + 1.0 uL well solution, protein solution: 6.5 mg/mL TAO3K in 0.7 mM ADP, 5 mM magnesium chloride, 100 mM sodium chloride, 25 mM Tris, pH 8.0, 2 mM BME, 0.3 mM EDTA, well solution: 20% PEG3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, cryoprotectant: 20% PEG1500
PH range: 6.7-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12708 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2015
RadiationMonochromator: Si(111) side scattering I-beam bent single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12708 Å / Relative weight: 1
ReflectionResolution: 1.5→38.1 Å / Num. obs: 59157 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.02 / Rrim(I) all: 0.042 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.534.40.61728890.7510.3270.70199.8
8.22-38.13.80.0294230.9960.0170.03498.5

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U5R

1u5r


Resolution: 1.5→38.1 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.419 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 2959 5 %RANDOM
Rwork0.1856 ---
obs0.187 56151 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.24 Å2 / Biso mean: 24.183 Å2 / Biso min: 11.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2--0.55 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.5→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 47 246 2766
Biso mean--19.13 34.49 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192606
X-RAY DIFFRACTIONr_bond_other_d0.0020.022469
X-RAY DIFFRACTIONr_angle_refined_deg2.3831.9663537
X-RAY DIFFRACTIONr_angle_other_deg1.16435690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29623.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11215451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1251514
X-RAY DIFFRACTIONr_chiral_restr0.1460.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212906
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02609
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 211 -
Rwork0.264 4095 -
all-4306 -
obs--99.17 %

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