[English] 日本語
Yorodumi
- PDB-8gw3: Crystal structure of human TAK1 kinase domain fused with TAB1 -

+
Open data


ID or keywords:

Loading...

-
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


histone kinase activity / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / linear polyubiquitin binding / interleukin-17A-mediated signaling pathway / MAP kinase kinase kinase kinase activity / cardiac septum development / I-kappaB phosphorylation / mitogen-activated protein kinase kinase kinase / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway ...histone kinase activity / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / linear polyubiquitin binding / interleukin-17A-mediated signaling pathway / MAP kinase kinase kinase kinase activity / 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 / positive regulation of cGAS/STING signaling pathway / JUN kinase kinase kinase activity / coronary vasculature development / ATAC complex / positive regulation of vascular associated smooth muscle cell migration / anoikis / non-canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / aorta development / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor 4 signaling pathway / protein serine/threonine phosphatase activity / cytoplasmic pattern recognition receptor signaling pathway / mitogen-activated protein kinase p38 binding / p38MAPK cascade / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / positive regulation of macroautophagy / positive regulation of JUN kinase activity / cellular response to angiotensin / MAP kinase activity / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / positive regulation of cell size / heart morphogenesis / stress-activated MAPK cascade / positive regulation of vascular associated smooth muscle cell proliferation / JNK cascade / positive regulation of cell cycle / protein serine/threonine kinase binding / 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 / transforming growth factor beta receptor signaling pathway / TRAF6-mediated induction of TAK1 complex within TLR4 complex / protein serine/threonine kinase activator activity / 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 / transcription coactivator binding / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / NOD1/2 Signaling Pathway / positive regulation of T cell cytokine production / receptor tyrosine kinase binding / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / MAPK cascade / Downstream TCR signaling / cellular response to tumor necrosis factor / T cell receptor signaling pathway / Ca2+ pathway / scaffold protein binding / DNA-binding transcription factor binding / molecular adaptor activity / cellular response to hypoxia / 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 / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more