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- PDB-5e7r: Crystal structure of TL10-81 bound to TAK1-TAB1 -

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Basic information

Entry
Database: PDB / ID: 5e7r
TitleCrystal structure of TL10-81 bound to TAK1-TAB1
ComponentsTAK1 kinase - TAB1 chimera fusion protein
KeywordsTRANSFERASE/TRANSFERASE inhibitor / Mitogen-activated protein kinase kinase kinase 7/TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


histone kinase activity / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of cGAS/STING signaling pathway / interleukin-17A-mediated signaling pathway / MAP kinase kinase kinase kinase activity / linear polyubiquitin binding / cardiac septum development / I-kappaB phosphorylation / mitogen-activated protein kinase kinase kinase / interleukin-33-mediated signaling pathway ...histone kinase activity / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of cGAS/STING signaling pathway / interleukin-17A-mediated signaling pathway / MAP kinase kinase kinase kinase activity / linear polyubiquitin binding / cardiac septum development / I-kappaB phosphorylation / mitogen-activated protein kinase kinase kinase / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / TRIF-dependent toll-like receptor signaling pathway / type II transforming growth factor beta receptor binding / coronary vasculature development / ATAC complex / cellular response to angiotensin / positive regulation of vascular associated smooth muscle cell migration / cytoplasmic pattern recognition receptor signaling pathway / aorta development / anoikis / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / non-canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / stimulatory C-type lectin receptor signaling pathway / p38MAPK cascade / Fc-epsilon receptor signaling pathway / positive regulation of macroautophagy / positive regulation of cell size / MAP kinase kinase kinase activity / MAP kinase activity / positive regulation of cell cycle / canonical NF-kappaB signal transduction / heart morphogenesis / protein serine/threonine kinase binding / stress-activated MAPK cascade / positive regulation of JUN kinase activity / positive regulation of vascular associated smooth muscle cell proliferation / 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 / TICAM1,TRAF6-dependent induction of TAK1 complex / positive regulation of interleukin-2 production / TRAF6-mediated induction of TAK1 complex within TLR4 complex / protein serine/threonine kinase activator activity / transforming growth factor beta receptor signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / activated TAK1 mediates p38 MAPK activation / lung development / Activation of NF-kappaB in B cells / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of protein serine/threonine kinase activity / positive regulation of T cell cytokine production / receptor tyrosine kinase binding / CLEC7A (Dectin-1) signaling / transcription coactivator binding / FCERI mediated NF-kB activation / Interleukin-1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / MAPK cascade / Downstream TCR signaling / cellular response to tumor necrosis factor / T cell receptor signaling pathway / Ca2+ pathway / cellular response to hypoxia / scaffold protein binding / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor binding / in utero embryonic development / positive regulation of MAPK cascade / molecular adaptor activity / endosome membrane / Ub-specific processing proteases / defense response to bacterium / nuclear speck / inflammatory response / immune 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 / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 7 / : / 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 ...Mitogen-activated protein (MAP) kinase kinase kinase 7 / : / 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 / 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. / 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-5KW / 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: 2.11 Å
AuthorsGurbani, D. / Hunter, J.C. / Tan, L. / Chen, Z. / Westover, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)CPRIT R1207 and CPRIT RP140233 United States
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: Structure-guided development of covalent TAK1 inhibitors.
Authors: Tan, L. / Gurbani, D. / Weisberg, E.L. / Hunter, J.C. / Li, L. / Jones, D.S. / Ficarro, S.B. / Mowafy, S. / Tam, C.P. / Rao, S. / Du, G. / Griffin, J.D. / Sorger, P.K. / Marto, J.A. / Westover, K.D. / Gray, N.S.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAK1 kinase - TAB1 chimera fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9512
Polymers35,4641
Non-polymers4871
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.179, 134.093, 149.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein TAK1 kinase - TAB1 chimera fusion protein / 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: 35463.867 Da / Num. of mol.: 1
Fragment: UNP O43318 residues 31-303, UNP Q15750 residues 468-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K7, TAK1, TAB1, MAP3K7IP1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O43318, UniProt: Q15750, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-5KW / 2-chloro-N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}acetamide


Mass: 487.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24Cl2N6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.07 Å3/Da / Density % sol: 69.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.65-0.75 M sodium citrate pH 7.0, 0.2 M NaCl, 0.1 M Tris pH 7.0, and 5mM adenosine. Adenosine bound TAK1-TAB1 crystals are backsoaked with inhibitor

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 32105 / % possible obs: 96.7 % / Redundancy: 8 % / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.088 / Net I/σ(I): 6.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.561 / Rpim(I) all: 0.553 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YIY

2yiy


Resolution: 2.11→42.148 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1282 4 %
Rwork0.22 --
obs0.221 32069 94.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→42.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 32 52 2253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072269
X-RAY DIFFRACTIONf_angle_d0.9563080
X-RAY DIFFRACTIONf_dihedral_angle_d13.3551342
X-RAY DIFFRACTIONf_chiral_restr0.05320
X-RAY DIFFRACTIONf_plane_restr0.007391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1096-2.19410.29111140.3152726X-RAY DIFFRACTION76
2.1941-2.29390.35591440.32693512X-RAY DIFFRACTION98
2.2939-2.41480.23961460.24853525X-RAY DIFFRACTION98
2.4148-2.56610.28321460.23923487X-RAY DIFFRACTION98
2.5661-2.76420.29131480.22643541X-RAY DIFFRACTION97
2.7642-3.04230.26991460.23563491X-RAY DIFFRACTION97
3.0423-3.48240.25591450.22883504X-RAY DIFFRACTION96
3.4824-4.38670.2071460.19453500X-RAY DIFFRACTION95
4.3867-42.15660.23051470.19743501X-RAY DIFFRACTION92

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