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

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Basic information

Entry
Database: PDB / ID: 5gjf
TitleCrystal structure of human TAK1/TAB1 fusion protein in complex with ligand 3
ComponentsTAK1 kinase - TAB1 chimera fusion protein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transferase-Transferase inhibitor complex / TAK1-TAB1 kinase
Function / homology
Function and homology information


nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of cGAS/STING signaling pathway / histone kinase activity / MAP kinase kinase kinase kinase activity / linear polyubiquitin binding / interleukin-17A-mediated signaling pathway / cardiac septum development / I-kappaB phosphorylation / mitogen-activated protein kinase kinase kinase / interleukin-33-mediated signaling pathway ...nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of cGAS/STING signaling pathway / histone kinase activity / MAP kinase kinase kinase kinase activity / linear polyubiquitin binding / interleukin-17A-mediated signaling pathway / cardiac septum development / I-kappaB phosphorylation / 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 / activation of NF-kappaB-inducing kinase activity / coronary vasculature development / ATAC complex / positive regulation of vascular associated smooth muscle cell migration / cellular response to angiotensin / anoikis / aorta development / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / toll-like receptor 4 signaling pathway / protein serine/threonine phosphatase activity / protein serine/threonine kinase binding / mitogen-activated protein kinase p38 binding / cytoplasmic pattern recognition receptor signaling pathway / p38MAPK cascade / non-canonical NF-kappaB signal transduction / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / positive regulation of macroautophagy / positive regulation of cell size / enzyme activator activity / MAP kinase kinase kinase activity / MAP kinase activity / canonical NF-kappaB signal transduction / stress-activated MAPK cascade / positive regulation of cell cycle / heart morphogenesis / positive regulation of JUN kinase activity / JNK cascade / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / 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 / positive regulation of interleukin-2 production / 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 / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / positive regulation of protein serine/threonine kinase activity / transcription coactivator binding / receptor tyrosine kinase binding / CLEC7A (Dectin-1) signaling / positive regulation of T cell cytokine production / FCERI mediated NF-kB activation / Interleukin-1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / MAPK cascade / Downstream TCR signaling / Ca2+ pathway / cellular response to tumor necrosis factor / cellular response to hypoxia / T cell receptor signaling pathway / 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 / nuclear speck / 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 / protein-containing complex binding / endoplasmic reticulum membrane / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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-6V4 / 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: 2.89 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)36,1302
Polymers35,5311
Non-polymers5991
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14150 Å2
Unit cell
Length a, b, c (Å)58.070, 132.960, 141.460
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-6V4 / N-(2-isopropoxy-4-(4-methylpiperazine-1-carbonyl)phenyl)-2-(3-(3-phenylureido)phenyl)thiazole-4-carboxamide


Mass: 598.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H34N6O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.94M sodium potassium phosphate, 20%(v/v) Glycerol as cryoprotectant

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→48.441 Å / Num. all: 12633 / Num. obs: 12633 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.153 / Rsym value: 0.142 / Net I/av σ(I): 5.182 / Net I/σ(I): 12.7 / Num. measured all: 90311
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.89-2.977.21.2220.6199.7
2.97-3.057.30.9450.8199.6
3.05-3.137.30.7321199.9
3.13-3.237.30.6041.2199.5
3.23-3.347.30.4911.51100
3.34-3.457.30.3672.1199.7
3.45-3.587.20.2532.9199.9
3.58-3.737.20.1913.91100
3.73-3.97.10.14951100
3.9-4.097.20.1186.31100
4.09-4.317.20.0957.71100
4.31-4.577.20.0759.7199.8
4.57-4.897.10.0769.61100
4.89-5.287.20.0769.7199.8
5.28-5.787.10.0848.71100
5.78-6.4670.074101100
6.46-7.4670.05812.31100
7.46-9.146.80.04116.31100
9.14-12.926.40.03319.5199.5
12.92-48.4415.40.04611198

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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: 2.89→48.44 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 12.559 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.56 / ESU R Free: 0.305
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 615 4.9 %RANDOM
Rwork0.1977 ---
obs0.1994 12018 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 140.77 Å2 / Biso mean: 64.998 Å2 / Biso min: 23.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å2-
2---0.07 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 2.89→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 43 13 2367
Biso mean--72.21 43.19 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192425
X-RAY DIFFRACTIONr_bond_other_d0.0010.022266
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9393300
X-RAY DIFFRACTIONr_angle_other_deg0.87735201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6585295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81623.19697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76615371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7071513
X-RAY DIFFRACTIONr_chiral_restr0.0620.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_mcbond_it2.7346.6551189
X-RAY DIFFRACTIONr_mcbond_other2.7356.6531188
X-RAY DIFFRACTIONr_mcangle_it4.8149.9681481
LS refinement shellResolution: 2.89→2.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 52 -
Rwork0.298 848 -
all-900 -
obs--99.67 %

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