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

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Basic information

Entry
Database: PDB / ID: 4lop
TitleStructural basis of autoactivation of p38 alpha induced by TAB1 (Tetragonal crystal form)
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


positive regulation of cGAS/STING signaling pathway / 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 ...positive regulation of cGAS/STING signaling pathway / 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 / coronary vasculature development / VEGFA-VEGFR2 Pathway / kinase activator activity / aorta development / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / cartilage condensation / cellular response to UV-B / protein serine/threonine phosphatase activity / 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 / 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 dietary excess / response to muramyl dipeptide / MAP kinase activity / regulation of ossification / 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 / 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 / transforming growth factor beta receptor signaling pathway / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / placenta development / lung development / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cellular response to virus / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / MAPK cascade / cellular response to tumor necrosis factor / kinase activity / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis / in utero embryonic development / cellular response to lipopolysaccharide / response to lipopolysaccharide / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / protein kinase activity / intracellular signal transduction / nuclear speck
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 / L(+)-TARTARIC ACID / 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: 2.049 Å
AuthorsChaikuad, A. / DeNicola, G.F. / Krojer, T. / Allerston, C.K. / 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

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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
K: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
L: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
M: 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)180,57629
Polymers177,9918
Non-polymers2,58521
Water15,583865
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)45,1727
Polymers44,4982
Non-polymers6755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-15 kcal/mol
Surface area17780 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)45,0847
Polymers44,4982
Non-polymers5875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-10 kcal/mol
Surface area17630 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)45,0847
Polymers44,4982
Non-polymers5875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-19 kcal/mol
Surface area17760 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)45,2348
Polymers44,4982
Non-polymers7376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-13 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.540, 86.540, 226.920
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(0.176045, -0.285413, -0.942097), (-0.29415, -0.92857, 0.226349), (-0.939406, 0.237271, -0.247425)10.63852, -72.09004, 35.49952
3given(-0.327356, 0.120172, 0.937228), (-0.895981, -0.35449, -0.267496), (0.300093, -0.927305, 0.223717)-4.64248, -37.83281, -23.08994
4given(-0.044289, 0.997393, 0.056979), (0.998979, 0.043704, 0.011469), (0.008949, 0.057429, -0.998309)41.58321, -40.72836, 36.89659

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Components

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

#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, 886 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-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.2 M Na/K tartrate, 0.1 M Bis-Tris propane, pH 6.5, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2012
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.783
11K, H, -L20.217
ReflectionResolution: 2.049→86.6 Å / Num. all: 103494 / Num. obs: 103422 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.5
Reflection shellResolution: 2.049→2.16 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.1 / Num. unique all: 14756 / % possible all: 97.1

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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: 2.049→86.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.434 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.034 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18753 5283 5.1 %RANDOM
Rwork0.14793 ---
all0.228 103422 --
obs0.14995 98138 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.418 Å2
Baniso -1Baniso -2Baniso -3
1-6.22 Å20 Å20 Å2
2--6.22 Å20 Å2
3----12.43 Å2
Refine analyzeLuzzati coordinate error obs: 0.258 Å
Refinement stepCycle: LAST / Resolution: 2.049→86.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11732 0 180 865 12777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212329
X-RAY DIFFRACTIONr_bond_other_d0.0030.028296
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.97716765
X-RAY DIFFRACTIONr_angle_other_deg1.0123.00420254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64451502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75823.943558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.864152055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7781574
X-RAY DIFFRACTIONr_chiral_restr0.0910.21879
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022481
LS refinement shellResolution: 2.049→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 375 -
Rwork0.202 6891 -
obs--94.08 %
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)
10.81360.2413-0.22860.943-0.33430.9956-0.05-0.0753-0.0417-0.0107-0.0082-0.0801-0.04190.07040.05820.00680.00370.00020.0399-0.00050.00911.3261-10.381839.0732
21.13340.09431.0960.360.01142.2982-0.00120.088-0.1071-0.03390.0117-0.04630.08430.0625-0.01050.0626-0.00770.00470.02580.00290.02925.2595-1.907915.0985
30.797-0.39740.120.8066-0.23860.478-0.06680.01640.16050.0117-0.0185-0.1112-0.15370.05470.08530.0753-0.0288-0.01370.05570.00940.066815.93141.242725.0198
40.72980.0880.79960.4509-0.13161.48540.0706-0.0743-0.15040.083-0.01140.00030.1941-0.0221-0.05910.13040.00810.00570.03030.00480.103325.5794-54.9166-3.9906
52.5401-0.88450.33761.4463-0.17250.91320.0222-0.2217-0.04220.20190.03540.3318-0.0285-0.2989-0.05770.1202-0.01160.01610.1124-0.00050.12693.7905-42.6448-16.8637
60.5424-0.02570.44590.5211-0.57912.02390.0524-0.0472-0.17230.00410.00280.04790.1949-0.0718-0.05520.1149-0.0279-0.00460.0395-0.02550.146313.0553-58.6618-15.0648
70.64930.20970.06940.6898-0.52521.3538-0.01770.0644-0.083-0.06830.04240.09550.017-0.131-0.02470.01440.0185-0.0060.07340.00560.0544-13.6868-18.999239.4541
81.5106-0.56210.00112.5479-0.33270.98960.00440.2325-0.3697-0.21140.0385-0.17890.3030.0707-0.0430.09860.02250.00770.1509-0.00320.2035-1.6158-38.575152.4107
90.35770.08840.49880.331-0.24051.83750.0304-0.0232-0.13020.00240.01460.05450.1886-0.0908-0.04490.0519-0.0080.02580.12970.02580.1593-16.5954-32.461750.1406
101.0043-0.15350.0421.46340.91251.62890.00090.0220.1116-0.0259-0.03150.0978-0.0543-0.05640.03060.0273-0.00750.00020.01950.00760.026228.1735-27.8005-5.1972
111.6866-0.20830.03062.2383-0.27411.78070.01860.0737-0.0958-0.0085-0.01940.13150.0656-0.04920.00080.0054-0.0093-0.00130.0295-0.00370.012242.2915-34.233713.5029
120.6541-0.31390.35650.599-0.2070.6156-0.05-0.03310.07060.08090.0041-0.0837-0.08830.05590.04590.0409-0.02240.00610.0516-0.01190.035342.6982-29.58719.5684
135.4182.88020.1783.5952-2.05652.26640.1415-0.0827-0.40010.0235-0.1714-0.18780.03430.16350.030.14450.0322-0.03050.16960.05860.1687-1.601-25.604670.4052
147.36641.7469-3.35262.9227-0.48415.20370.1606-0.2847-0.11870.2306-0.04320.3304-0.18130.1588-0.11740.090.02590.00280.0699-0.02030.0832-7.4724-10.684855.6398
155.99541.2771.03272.4187-1.06553.8882-0.1363-0.19360.0586-0.29070.16650.1350.07490.0338-0.03020.1023-0.0507-0.010.13790.03040.098419.3762-42.6452-34.9343
161.87780.9508-0.39263.4103-1.04360.3276-0.04240.1814-0.3183-0.1046-0.0201-0.17640.04650.0020.06240.12020.0466-0.01560.1607-0.01430.090434.0986-48.0202-19.5472
174.7853-1.6478-3.17614.0918-0.86144.29030.04750.10680.0588-0.0010.0218-0.188-0.1828-0.0397-0.06930.13640.0419-0.03950.11370.04880.237-6.436916.561623.4841
1812.12184.9222-4.79747.4817-4.06417.8729-0.1578-0.66780.00390.1562-0.11610.27580.2028-0.30450.27380.12970.0725-0.00360.185-0.01150.0997-2.03746.404839.9623
194.55360.50710.31553.12540.27917.08120.0644-0.1294-0.23420.1766-0.1623-0.3189-0.0034-0.21870.09790.15070.0543-0.02980.1374-0.01010.201659.567-46.125215.1517
205.14271.8823-0.545517.30741.92545.1780.14220.1108-1.0412-0.0653-0.03190.04620.4479-0.3745-0.11030.23690.0126-0.02230.2358-0.01190.24650.8098-41.6266-2.651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 140
2X-RAY DIFFRACTION2A141 - 267
3X-RAY DIFFRACTION3A268 - 353
4X-RAY DIFFRACTION4B4 - 172
5X-RAY DIFFRACTION5B173 - 265
6X-RAY DIFFRACTION6B266 - 353
7X-RAY DIFFRACTION7C3 - 171
8X-RAY DIFFRACTION8C172 - 264
9X-RAY DIFFRACTION9C265 - 353
10X-RAY DIFFRACTION10D3 - 111
11X-RAY DIFFRACTION11D112 - 228
12X-RAY DIFFRACTION12D229 - 353
13X-RAY DIFFRACTION13K384 - 395
14X-RAY DIFFRACTION14K404 - 412
15X-RAY DIFFRACTION15L384 - 395
16X-RAY DIFFRACTION16L404 - 412
17X-RAY DIFFRACTION17M385 - 394
18X-RAY DIFFRACTION18M404 - 411
19X-RAY DIFFRACTION19N384 - 394
20X-RAY DIFFRACTION20N404 - 411

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