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- PDB-8gw3: Crystal structure of human TAK1 kinase domain fused with TAB1 -

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Basic information

Entry
Database: PDB / ID: 8gw3
TitleCrystal structure of human TAK1 kinase domain fused with TAB1
ComponentsMitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
KeywordsSIGNALING PROTEIN / protein kinase
Function / homology
Function and homology information


I-kappaB phosphorylation / histone kinase activity / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / linear polyubiquitin binding / cardiac septum development / interleukin-17A-mediated signaling pathway / MAP kinase kinase kinase kinase activity / mitogen-activated protein kinase kinase kinase / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway ...I-kappaB phosphorylation / histone kinase activity / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / linear polyubiquitin binding / cardiac septum development / interleukin-17A-mediated signaling pathway / MAP kinase kinase kinase kinase activity / mitogen-activated protein kinase kinase kinase / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / type II transforming growth factor beta receptor binding / TRIF-dependent toll-like receptor signaling pathway / positive regulation of cGAS/STING signaling pathway / coronary vasculature development / ATAC complex / positive regulation of vascular associated smooth muscle cell migration / non-canonical NF-kappaB signal transduction / anoikis / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / aorta development / toll-like receptor 4 signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / mitogen-activated protein kinase p38 binding / p38MAPK cascade / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / positive regulation of JUN kinase activity / protein serine/threonine phosphatase activity / cellular response to angiotensin / positive regulation of macroautophagy / MAP kinase activity / positive regulation of cell size / canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / heart morphogenesis / stress-activated MAPK cascade / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of cell cycle / JNK cascade / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of interleukin-2 production / TICAM1,TRAF6-dependent induction of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / transforming growth factor beta receptor signaling pathway / lung development / protein serine/threonine kinase binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / protein serine/threonine kinase activator activity / TNFR1-induced NF-kappa-B signaling pathway / activated TAK1 mediates p38 MAPK activation / Activation of NF-kappaB in B cells / positive regulation of non-canonical NF-kappaB signal transduction / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of T cell cytokine production / receptor tyrosine kinase binding / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / transcription coactivator binding / Interleukin-1 signaling / cellular response to tumor necrosis factor / Downstream TCR signaling / T cell receptor signaling pathway / MAPK cascade / Ca2+ pathway / scaffold protein binding / cellular response to hypoxia / molecular adaptor activity / DNA-binding transcription factor binding / in utero embryonic development / positive regulation of canonical NF-kappaB signal transduction / endosome membrane / positive regulation of MAPK cascade / Ub-specific processing proteases / defense response to bacterium / immune response / inflammatory response / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / magnesium ion binding / endoplasmic reticulum / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site ...: / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 7 / TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLiu, J. / Sun, W. / Gao, J.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82188101 China
National Natural Science Foundation of China (NSFC)91849204 China
National Natural Science Foundation of China (NSFC)21837004 China
National Natural Science Foundation of China (NSFC)92049303 China
National Natural Science Foundation of China (NSFC)32170755 China
National Natural Science Foundation of China (NSFC)32071297 China
CitationJournal: To Be Published
Title: Crystal structure of human TAK1 kinase domain fused with TAB1
Authors: Liu, J. / Sun, W. / Gao, J.
History
DepositionSep 16, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
B: Mitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
C: Mitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
D: Mitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1


Theoretical massNumber of molelcules
Total (without water)146,9614
Polymers146,9614
Non-polymers00
Water7,548419
1
A: Mitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1


Theoretical massNumber of molelcules
Total (without water)36,7401
Polymers36,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1


Theoretical massNumber of molelcules
Total (without water)36,7401
Polymers36,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1


Theoretical massNumber of molelcules
Total (without water)36,7401
Polymers36,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1


Theoretical massNumber of molelcules
Total (without water)36,7401
Polymers36,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.814, 196.460, 72.415
Angle α, β, γ (deg.)90.000, 115.240, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 27 through 28 or (resid 29...
d_2ens_1(chain "B" and (resid 27 through 28 or (resid 29...
d_3ens_1(chain "C" and ((resid 27 and (name N or name...
d_4ens_1(chain "D" and (resid 27 through 38 or (resid 39...

NCS oper:
IDCodeMatrixVector
1given(-0.908533671474, -0.137151875545, -0.39465925915), (0.150070192722, -0.988673540695, -0.0018886995489), (-0.389930128426, -0.0609425382155, 0.918825610212)-26.872786073, -15.2940877128, 10.023598406
2given(0.548533489215, 0.21244612604, -0.808688849151), (0.227213328307, -0.968660645383, -0.100352665765), (-0.804664597612, -0.128698087076, -0.57961339506)40.3620988963, -63.1231727507, 60.3199787482
3given(-0.193497513955, -0.0484936547101, 0.979901565233), (-0.188124573993, 0.982078393324, 0.0114531229673), (-0.96289555859, -0.182127413694, -0.199152575751)-15.3835102126, 51.7773334707, 51.8419200578

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Components

#1: Protein
Mitogen-activated protein kinase kinase kinase 7, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 / Transforming growth factor-beta-activated kinase 1 / TGF-beta-activated kinase 1 / Mitogen- ...Transforming growth factor-beta-activated kinase 1 / TGF-beta-activated kinase 1 / Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase 1-binding protein 1 / TAK1-binding protein 1


Mass: 36740.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: TAK1 kinase domain (15-303), TAB1(468-504) / Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K7, TAK1, TAB1, MAP3K7IP1 / Production host: Escherichia coli (E. coli)
References: UniProt: O43318, UniProt: Q15750, mitogen-activated protein kinase kinase kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2% (v/v) Tacsimate pH7.0, 0.1M HEPES pH 7.5, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.05→65.5 Å / Num. obs: 70634 / % possible obs: 99.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 40.87 Å2 / CC1/2: 1 / Rpim(I) all: 0.029 / Net I/σ(I): 17.9
Reflection shellResolution: 2.05→2.25 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3532 / CC1/2: 0.669 / Rpim(I) all: 0.49 / % possible all: 53.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20210323data reduction
Aimless1.12.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EVA

2eva


Resolution: 2.05→58.63 Å / SU ML: 0.3125 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.2765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2582 3539 5.02 %
Rwork0.2213 66961 -
obs0.2232 70500 69.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.87 Å2
Refinement stepCycle: LAST / Resolution: 2.05→58.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9039 0 0 419 9458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00889298
X-RAY DIFFRACTIONf_angle_d1.074712678
X-RAY DIFFRACTIONf_chiral_restr0.05691399
X-RAY DIFFRACTIONf_plane_restr0.00921611
X-RAY DIFFRACTIONf_dihedral_angle_d5.61331270
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.858610503034
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.20140607511
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.20847932904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.220510.395539X-RAY DIFFRACTION1.01
2.08-2.110.731330.3779119X-RAY DIFFRACTION2.99
2.11-2.140.3778140.3535295X-RAY DIFFRACTION7.72
2.14-2.170.6003220.3533559X-RAY DIFFRACTION14.32
2.17-2.210.3731370.3415844X-RAY DIFFRACTION22.06
2.21-2.250.4521720.32421284X-RAY DIFFRACTION32.9
2.25-2.290.32531120.33441757X-RAY DIFFRACTION46.13
2.29-2.330.34891300.32682095X-RAY DIFFRACTION54.43
2.33-2.380.3531210.32072458X-RAY DIFFRACTION63.33
2.38-2.430.31281470.32572579X-RAY DIFFRACTION67.66
2.43-2.490.35761780.31582803X-RAY DIFFRACTION72.5
2.49-2.550.3521490.31533068X-RAY DIFFRACTION79.53
2.55-2.620.36451570.3043335X-RAY DIFFRACTION85.25
2.62-2.70.36922030.29153584X-RAY DIFFRACTION93.25
2.7-2.780.32831980.29163780X-RAY DIFFRACTION98.17
2.78-2.880.34421950.27353810X-RAY DIFFRACTION98.69
2.88-30.31991830.26213888X-RAY DIFFRACTION99.44
3-3.140.27691880.25513866X-RAY DIFFRACTION99.29
3.14-3.30.30321900.25013852X-RAY DIFFRACTION99.14
3.3-3.510.27271990.22663788X-RAY DIFFRACTION97.51
3.51-3.780.22741780.19663840X-RAY DIFFRACTION99.09
3.78-4.160.22161960.17813833X-RAY DIFFRACTION98.77
4.16-4.760.20432070.1533812X-RAY DIFFRACTION97.88
4.76-60.2032340.17943841X-RAY DIFFRACTION99.22
6-58.630.20832250.18863832X-RAY DIFFRACTION98.14

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