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

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Basic information

Entry
Database: PDB / ID: 5gjg
TitleCrystal structure of human TAK1/TAB1 fusion protein in complex with ligand 4
ComponentsTAK1 kinase - TAB1 chimera fusion protein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transferase-Transferase inhibitor complex / TAK1-TAB1 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 / mitogen-activated protein kinase p38 binding / cytoplasmic pattern recognition receptor signaling pathway / 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 / positive regulation of interleukin-2 production / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / transforming growth factor beta receptor signaling pathway / protein serine/threonine kinase binding / lung development / 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 / positive regulation of MAPK cascade / endosome membrane / 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 / Phosphorylase Kinase; domain 1 ...: / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-6V5 / 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: 2.61 Å
AuthorsIrie, M. / Nakamura, M. / Fukami, T.A. / Matsuura, T. / Morishima, K.
CitationJournal: Chem.Pharm.Bull. / Year: 2016
Title: Development of a Method for Converting a TAK1 Type I Inhibitor into a Type II or c-Helix-Out Inhibitor by Structure-Based Drug Design (SBDD)
Authors: Muraoka, T. / Ide, M. / Irie, M. / Morikami, K. / Miura, T. / Nishihara, M. / Kashiwagi, H.
History
DepositionJun 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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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)36,1152
Polymers35,5311
Non-polymers5841
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13820 Å2
Unit cell
Length a, b, c (Å)58.030, 133.220, 146.750
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-6V5 / N-(2-isopropoxy-4-(4-methylpiperazine-1-carbonyl)phenyl)-2-(3-(phenylcarbamoyl)phenyl)thiazole-4-carboxamide


Mass: 583.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H33N5O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 294 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: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→41.93 Å / Num. all: 17613 / Num. obs: 17613 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Rsym value: 0.094 / Net I/av σ(I): 7.732 / Net I/σ(I): 18.7 / Num. measured all: 126645
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.61-2.687.10.8730.9196.3
2.68-2.757.40.731.1198.8
2.75-2.837.30.5651.4198.9
2.83-2.927.30.4181.8199.1
2.92-3.017.40.382199.6
3.01-3.127.30.263199.2
3.12-3.247.30.2113.6199.2
3.24-3.377.30.1564.9199.3
3.37-3.527.20.1126.8199.9
3.52-3.697.20.0868.9199.7
3.69-3.897.20.06611.2199.9
3.89-4.137.20.05213.8199.9
4.13-4.417.10.04415.3199.6
4.41-4.7770.04216.3199.6
4.77-5.2270.04216.1199.8
5.22-5.846.80.04115.8199.8
5.84-6.747.10.03719.41100
6.74-8.2570.02922.9199.8
8.25-11.676.80.0319.5199.7
11.67-41.9360.02822.7197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata processing
SCALA3.3.15data scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EVA

2eva


Resolution: 2.61→41.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.605 / SU ML: 0.173 / SU R Cruickshank DPI: 0.2662 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.218
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 892 5.1 %RANDOM
Rwork0.1806 ---
obs0.1826 16721 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 144.36 Å2 / Biso mean: 59.236 Å2 / Biso min: 25.36 Å2
Baniso -1Baniso -2Baniso -3
1--6.06 Å2-0 Å20 Å2
2---1.34 Å2-0 Å2
3---7.4 Å2
Refinement stepCycle: final / Resolution: 2.61→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 42 36 2302
Biso mean--70.68 46.1 -
Num. residues----289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192337
X-RAY DIFFRACTIONr_bond_other_d0.0020.022147
X-RAY DIFFRACTIONr_angle_refined_deg1.951.943187
X-RAY DIFFRACTIONr_angle_other_deg1.08734935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2865286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58123.69692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65215345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.837159
X-RAY DIFFRACTIONr_chiral_restr0.1080.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212614
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02531
X-RAY DIFFRACTIONr_mcbond_it5.4196.0611153
X-RAY DIFFRACTIONr_mcbond_other5.4246.0581152
X-RAY DIFFRACTIONr_mcangle_it8.3689.0591436
LS refinement shellResolution: 2.61→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 71 -
Rwork0.318 1169 -
all-1240 -
obs--96.35 %

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