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- PDB-4loq: Structural basis of autoactivation of p38 alpha induced by TAB1 (... -

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Basic information

Entry
Database: PDB / ID: 4loq
TitleStructural basis of autoactivation of p38 alpha induced by TAB1 (Tetragonal crystal form with bound sulphate)
Components
  • Mitogen-activated protein kinase 14MAPK14
  • TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / protein kinase / kinase-regulatory protein complex / MAPK / autoactivation / autophosphorylation
Function / homology
Function and homology information


IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TNFR1-induced NF-kappa-B signaling pathway / cardiac septum development / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling ...IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TNFR1-induced NF-kappa-B signaling pathway / cardiac septum development / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Myogenesis / Ub-specific processing proteases / kinase activator activity / coronary vasculature development / VEGFA-VEGFR2 Pathway / aorta development / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / protein serine/threonine phosphatase activity / cartilage condensation / cellular response to UV-B / stress-activated protein kinase signaling cascade / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / glucose import / response to dietary excess / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / non-canonical NF-kappaB signal transduction / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / regulation of ossification / MAP kinase activity / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / heart morphogenesis / skeletal muscle tissue development / signal transduction in response to DNA damage / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / Neutrophil degranulation / positive regulation of interleukin-12 production / protein serine/threonine kinase activator activity / osteoclast differentiation / transforming growth factor beta receptor signaling pathway / positive regulation of erythrocyte differentiation / placenta development / DNA damage checkpoint signaling / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / lung development / negative regulation of canonical Wnt signaling pathway / response to insulin / bone development / cell morphogenesis / osteoblast differentiation / cellular response to virus / spindle pole / positive regulation of protein import into nucleus / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / MAPK cascade / cellular response to tumor necrosis factor / kinase activity / protein phosphatase binding / peptidyl-serine phosphorylation / angiogenesis / cellular response to lipopolysaccharide / in utero embryonic development / response to lipopolysaccharide / positive regulation of MAPK cascade / transcription by RNA polymerase II / molecular adaptor activity / protein kinase activity / intracellular signal transduction
Similarity search - Function
Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. ...Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-SB4 / Mitogen-activated protein kinase 14 / TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.319 Å
AuthorsChaikuad, A. / DeNicola, G.F. / Yue, W.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Marber, M.S. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Mechanism and consequence of the autoactivation of p38 alpha mitogen-activated protein kinase promoted by TAB1.
Authors: De Nicola, G.F. / Martin, E.D. / Chaikuad, A. / Bassi, R. / Clark, J. / Martino, L. / Verma, S. / Sicard, P. / Tata, R. / Atkinson, R.A. / Knapp, S. / Conte, M.R. / Marber, M.S.
History
DepositionJul 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Oct 23, 2013Group: Database references
Revision 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
B: Mitogen-activated protein kinase 14
C: Mitogen-activated protein kinase 14
D: Mitogen-activated protein kinase 14
M: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
L: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
K: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
N: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,54727
Polymers177,9918
Non-polymers2,55719
Water8,251458
1
A: Mitogen-activated protein kinase 14
M: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0906
Polymers44,4982
Non-polymers5934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-46 kcal/mol
Surface area18150 Å2
MethodPISA
2
B: Mitogen-activated protein kinase 14
L: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2779
Polymers44,4982
Non-polymers7797
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-40 kcal/mol
Surface area18340 Å2
MethodPISA
3
C: Mitogen-activated protein kinase 14
K: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0906
Polymers44,4982
Non-polymers5934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-43 kcal/mol
Surface area18000 Å2
MethodPISA
4
D: Mitogen-activated protein kinase 14
N: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0906
Polymers44,4982
Non-polymers5934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-45 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.100, 87.100, 228.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.344322, -0.889387, 0.30072), (0.131684, -0.36289, -0.92248), (0.92957, -0.278031, 0.24207)-28.24379, -36.1341, -1.14437
3given(-0.862401, -0.384422, -0.329369), (-0.382513, 0.068677, 0.921394), (-0.331584, 0.920599, -0.206274)5.42626, -48.49596, 58.17466
4given(-0.045335, 0.998962, 0.004479), (0.998515, 0.045178, 0.030459), (0.030225, 0.005854, -0.999526)43.34336, -41.73178, 34.87913

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDMLKN

#1: Protein
Mitogen-activated protein kinase 14 / MAPK14 / MAP kinase 14 / MAPK 14 / CRK1 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha


Mass: 41395.211 Da / Num. of mol.: 4 / Fragment: kinase domain (1-360)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MAPK14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli (E. coli)
References: UniProt: P47811, mitogen-activated protein kinase
#2: Protein/peptide
TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 / Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase ...Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase 1-binding protein 1 / TAK1-binding protein 1


Mass: 3102.515 Da / Num. of mol.: 4 / Fragment: residues 384-412 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8CF89

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Non-polymers , 4 types, 477 molecules

#3: Chemical
ChemComp-SB4 / 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE / SB220025


Mass: 338.382 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19FN6
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% Medium-molecular weight PEG Smears, 0.2 M Ammonium sulphate, 0.01 M CdCl2, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 9, 2012
RadiationMonochromator: single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.708
11K, H, -L20.292
ReflectionResolution: 2.319→4355 Å / Num. all: 72211 / Num. obs: 72157 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.4
Reflection shellResolution: 2.319→2.45 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2 / Num. unique all: 10608 / % possible all: 99.6

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QUE

3que


Resolution: 2.319→42.78 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.168 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.079 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23569 3632 5 %RANDOM
Rwork0.19182 ---
all0.291 72157 --
obs0.19403 68524 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.704 Å2
Baniso -1Baniso -2Baniso -3
1-24.78 Å20 Å20 Å2
2--24.78 Å20 Å2
3----49.57 Å2
Refine analyzeLuzzati coordinate error obs: 0.393 Å
Refinement stepCycle: LAST / Resolution: 2.319→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11740 0 168 458 12366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212311
X-RAY DIFFRACTIONr_bond_other_d0.0030.028275
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.97616749
X-RAY DIFFRACTIONr_angle_other_deg1.0573.00420182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05851493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90823.797561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.065152055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7031578
X-RAY DIFFRACTIONr_chiral_restr0.0770.21873
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113511
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022495
LS refinement shellResolution: 2.319→2.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 263 -
Rwork0.238 5023 -
obs--97.6 %
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)
10.88230.056-0.24950.9165-0.36891.0092-0.0476-0.0188-0.0212-0.04640.0306-0.0532-0.17180.09140.01710.0638-0.0249-0.02890.0136-0.0040.148610.2955-7.504132.8376
20.51760.13930.91830.72411.29853.53830.03580.09480.12420.03880.0292-0.1987-0.06590.1027-0.06490.13410.0236-0.0180.08370.04910.2417-0.08581.10634.6629
30.8159-0.50580.16691.5279-0.44710.6183-0.0268-0.03860.1825-0.0830.0017-0.1426-0.17590.06870.02520.0979-0.03890.01310.0348-0.01430.270216.16991.574725.5396
41.4295-1.50420.11024.2277-0.9750.31520.0287-0.0692-0.3673-0.0178-0.00990.15570.07460.0512-0.01880.27490.0838-0.10470.1676-0.01910.355735.0084-53.31234.5942
50.5974-0.0540.40360.2689-0.02351.27620.111-0.0681-0.18780.0684-0.08270.05770.39570.1503-0.02820.2627-0.008-0.01090.08960.00030.362521.8247-56.296-6.7926
60.69780.08020.01710.9097-0.10161.33490.06330.0333-0.1417-0.0127-0.05080.16330.1308-0.1101-0.01250.1304-0.0506-0.00120.0341-0.04760.35728.1022-50.9661-16.6941
70.73450.33130.11161.1369-0.99851.9488-0.07310.0039-0.2262-0.08750.04320.0630.0244-0.18590.02990.01190.00410.01520.0343-0.01070.2703-10.8563-22.88241.9217
86.01274.894-7.23044.078-6.15959.5011-0.0174-0.1056-0.76860.0534-0.0819-0.3632-0.09890.0260.09920.12860.07170.01110.04670.0810.89963.3464-43.428758.583
90.42520.14140.45720.637-0.23121.85580.005-0.0794-0.19330.0482-0.00130.0670.1369-0.1396-0.00370.0279-0.01030.04040.09230.0120.4028-15.5127-32.912750.8517
101.4878-0.02210.12981.39370.28241.59950.00770.02870.0556-0.0403-0.072-0.04630.010.25250.06440.0421-0.02760.01720.07650.00680.150728.4977-28.772-5.8917
111.1003-0.26960.34391.8068-0.66052.36980.04270.0075-0.00080.1157-0.098-0.0710.16410.30120.05530.0563-0.03980.0120.1614-0.0170.275843.2239-36.85118.2264
120.8616-0.28950.24440.659-0.22370.8293-0.09670.03560.170.0356-0.0353-0.3606-0.06990.33110.1320.1086-0.07610.00220.1728-0.01350.384443.3029-24.110710.1789
134.9473-0.99843.10584.6535-3.10693.33460.3489-0.2167-0.5688-0.3665-0.2876-0.31980.35720.0709-0.06120.1718-0.0617-0.0020.14220.04980.3636-1.4383-24.992870.5376
1411.19451.2661-6.39412.11973.32112.08510.5318-0.27040.1389-0.3284-0.14650.0113-1.24540.1056-0.38520.2290.00440.13030.1436-0.09880.4142-8.1994-10.722556.1964
1510.4928-5.7559-2.68247.95620.9241.13290.45930.10940.1248-0.7538-0.46930.106-0.2299-0.1540.01010.22760.03620.00920.2358-0.01910.30119.5332-43.8846-35.4334
160.3251-0.294-1.4890.32291.44837.1467-0.1231-0.1795-0.0370.19890.3009-0.05350.69550.9952-0.17780.28410.1860.03050.3625-0.08980.469633.8707-50.3565-21.0222
174.8637-0.9868-0.85971.33133.08527.9032-0.08150.13410.16710.1657-0.0545-0.04120.1628-0.15890.1360.24120.0482-0.11990.05460.04090.3358-6.875616.791623.3211
1810.32595.7997-5.321910.6694-1.51723.0373-0.28590.210.1635-0.20320.13871.26820.1563-0.09540.14720.13720.0335-0.08110.12820.01370.3888-1.97736.540639.8828
194.9674-0.57523.83152.25930.993.89340.2275-0.2197-0.2457-0.0825-0.08670.06550.1335-0.2394-0.14080.3107-0.0090.03540.37230.02710.511760.5725-46.968113.4029
200.1569-0.9535-0.446820.79663.83791.3622-0.02810.0534-0.1118-0.2529-0.1495-0.61360.0369-0.15450.17750.383-0.03860.04130.44820.02080.40450.8483-42.7435-3.6664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 218
2X-RAY DIFFRACTION2A219 - 269
3X-RAY DIFFRACTION3A270 - 354
4X-RAY DIFFRACTION4B3 - 44
5X-RAY DIFFRACTION5B45 - 173
6X-RAY DIFFRACTION6B174 - 353
7X-RAY DIFFRACTION7C4 - 227
8X-RAY DIFFRACTION8C228 - 245
9X-RAY DIFFRACTION9C259 - 353
10X-RAY DIFFRACTION10D4 - 110
11X-RAY DIFFRACTION11D111 - 273
12X-RAY DIFFRACTION12D274 - 354
13X-RAY DIFFRACTION13K384 - 395
14X-RAY DIFFRACTION14K403 - 412
15X-RAY DIFFRACTION15L384 - 395
16X-RAY DIFFRACTION16L403 - 412
17X-RAY DIFFRACTION17M385 - 394
18X-RAY DIFFRACTION18M404 - 411
19X-RAY DIFFRACTION19N385 - 394
20X-RAY DIFFRACTION20N404 - 411

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