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- PDB-5jgb: Crystal structure of human TAK1/TAB1 fusion protein in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5jgb
TitleCrystal structure of human TAK1/TAB1 fusion protein in complex with ligand 10
ComponentsTAK1 kinase - TAB1 chimera fusion protein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transferase-Transferase inhibitor complex / TAK1-TAB1 kinase
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 / Activation of NF-kappaB in B cells / lung development / 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-6JV / 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 / molecular replacement / Resolution: 2.8 Å
AuthorsIrie, M. / Nakamura, M. / Fukami, T.A. / Matsuura, T. / Morishima, K.
CitationJournal: Bioorg.Med.Chem. / Year: 2016
Title: Discovery of a potent and highly selective transforming growth factor beta receptor-associated kinase 1 (TAK1) inhibitor by structure based drug design (SBDD)
Authors: Muraoka, T. / Ide, M. / Morikami, K. / Irie, M. / Nakamura, M. / Miura, T. / Kamikawa, T. / Nishihara, M. / Kashiwagi, H.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)36,0162
Polymers35,5311
Non-polymers4851
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14190 Å2
Unit cell
Length a, b, c (Å)58.711, 134.970, 143.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein TAK1 kinase - TAB1 chimera fusion protein


Mass: 35530.953 Da / Num. of mol.: 1 / Fragment: UNP residues 31-303,UNP residues 468-504
Source method: isolated from a genetically manipulated source
Details: fusion of Mitogen-activated protein kinase kinase kinase 7,TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K7, TAK1, TAB1, MAP3K7IP1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O43318, UniProt: Q15750, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-6JV / N-(2-methoxy-4-{[3-(4-methylpiperazin-1-yl)propyl]carbamoyl}phenyl)-4-oxo-3,4-dihydrothieno[3,2-d]pyrimidine-7-carboxamide


Mass: 484.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N6O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.99 Å3/Da / Density % sol: 69.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 1.7M sodium potassium phosphate, 20%(v/v) Glycerol as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→98 Å / Num. obs: 13809 / % possible obs: 95.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Net I/av σ(I): 10.718 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.852.60.456150.4
2.85-2.92.70.4164.7
2.9-2.962.80.474177.4
2.96-3.0230.366188
3.02-3.083.10.383194.2
3.08-3.153.40.315197.2
3.15-3.233.70.262199.3
3.23-3.3240.267199.9
3.32-3.4240.211199.7
3.42-3.534.10.1621100
3.53-3.654.10.1361100
3.65-3.84.10.1171100
3.8-3.974.10.1199.7
3.97-4.184.10.0821100
4.18-4.444.10.07199.9
4.44-4.7940.066199.3
4.79-5.2740.066199.7
5.27-6.0340.065199.6
6.03-7.5940.05199.1
7.59-503.70.037197.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EVA

2eva


Resolution: 2.8→71.58 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / SU B: 12.005 / SU ML: 0.227 / SU R Cruickshank DPI: 0.4794 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.479 / ESU R Free: 0.303 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 688 5.1 %RANDOM
Rwork0.2006 ---
obs0.2026 12901 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.84 Å2 / Biso mean: 48.586 Å2 / Biso min: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.8→71.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 34 33 2355
Biso mean--65.18 36.26 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192394
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9523258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8365293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99122.84295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81915367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2031514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211820
X-RAY DIFFRACTIONr_mcbond_it1.964.9931178
X-RAY DIFFRACTIONr_mcangle_it3.5917.4791469
X-RAY DIFFRACTIONr_scbond_it1.8844.9251215
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 37 -
Rwork0.313 570 -
all-607 -
obs--59.45 %

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