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- PDB-5nzz: Crystal structure of phosphorylated p38aMAPK in complex with TAB1 -

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Basic information

Entry
Database: PDB / ID: 5nzz
TitleCrystal structure of phosphorylated p38aMAPK in complex with TAB1
Components
  • Mitogen-activated protein kinase 14
  • TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
KeywordsTRANSFERASE / MAPK activated phosphorylated P38 regulation
Function / homology
Function and homology information


p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / regulation of synaptic membrane adhesion / Regulation of MITF-M-dependent genes involved in pigmentation / NLRP1 inflammasome complex assembly / cartilage condensation ...p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / regulation of synaptic membrane adhesion / Regulation of MITF-M-dependent genes involved in pigmentation / NLRP1 inflammasome complex assembly / cartilage condensation / cell surface receptor protein serine/threonine kinase signaling pathway / ADP signalling through P2Y purinoceptor 1 / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / Myogenesis / Regulation of TP53 Activity through Phosphorylation / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / response to muramyl dipeptide / VEGFA-VEGFR2 Pathway / regulation of ossification / chondrocyte differentiation / fatty acid oxidation / striated muscle cell differentiation / stress-induced premature senescence / positive regulation of myoblast fusion / stress-activated protein kinase signaling cascade / skeletal muscle tissue development / positive regulation of cyclase activity / positive regulation of myotube differentiation / cellular response to UV-B / mitogen-activated protein kinase p38 binding / non-canonical NF-kappaB signal transduction / NFAT protein binding / regulation of cytokine production involved in inflammatory response / cellular response to lipoteichoic acid / p38MAPK cascade / response to dietary excess / positive regulation of cardiac muscle cell proliferation / response to muscle stretch / protein serine/threonine phosphatase activity / MAP kinase activity / cellular response to vascular endothelial growth factor stimulus / positive regulation of cGAS/STING signaling pathway / regulation of MAPK cascade / mitogen-activated protein kinase / lipopolysaccharide-mediated signaling pathway / positive regulation of brown fat cell differentiation / vascular endothelial growth factor receptor signaling pathway / pyroptotic inflammatory response / stress-activated MAPK cascade / positive regulation of myoblast differentiation / negative regulation of hippo signaling / placenta development / osteoclast differentiation / serine/threonine protein kinase complex / positive regulation of interleukin-12 production / cell morphogenesis / DNA damage checkpoint signaling / glucose metabolic process / signal transduction in response to DNA damage / Neutrophil degranulation / positive regulation of D-glucose import across plasma membrane / positive regulation of erythrocyte differentiation / tumor necrosis factor-mediated signaling pathway / response to insulin / protein serine/threonine kinase activator activity / 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 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / cellular response to ionizing radiation / canonical NF-kappaB signal transduction / negative regulation of canonical Wnt signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / cellular response to tumor necrosis factor / TNFR1-induced NF-kappa-B signaling pathway / bone development / cellular response to virus / activated TAK1 mediates p38 MAPK activation / positive regulation of protein import into nucleus / peptidyl-serine phosphorylation / NOD1/2 Signaling Pathway / osteoblast differentiation / TAK1-dependent IKK and NF-kappa-B activation / kinase activity / protein maturation / positive regulation of reactive oxygen species metabolic process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / angiogenesis / Interleukin-1 signaling / MAPK cascade / protein autophosphorylation / response to lipopolysaccharide / spindle pole / cellular response to lipopolysaccharide / protein phosphatase binding / molecular adaptor activity
Similarity search - Function
PPM-type phosphatase domain / Phosphatase 2c; 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 / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like ...PPM-type phosphatase domain / Phosphatase 2c; 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 / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 4-Layer Sandwich / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / NICKEL (II) ION / Mitogen-activated protein kinase 14 / TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å
AuthorsNichols, C.E. / De Nicola, G.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BHFBHF - FS/14/29/30896 - DE NICOLA United Kingdom
CitationJournal: JCI Insight / Year: 2018
Title: The TAB1-p38 alpha complex aggravates myocardial injury and can be targeted by small molecules.
Authors: De Nicola, G.F. / Bassi, R. / Nichols, C. / Fernandez-Caggiano, M. / Golforoush, P.A. / Thapa, D. / Anderson, R. / Martin, E.D. / Verma, S. / Kleinjung, J. / Laing, A. / Hutchinson, J.P. / ...Authors: De Nicola, G.F. / Bassi, R. / Nichols, C. / Fernandez-Caggiano, M. / Golforoush, P.A. / Thapa, D. / Anderson, R. / Martin, E.D. / Verma, S. / Kleinjung, J. / Laing, A. / Hutchinson, J.P. / Eaton, P. / Clark, J. / Marber, M.S.
History
DepositionMay 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
B: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
C: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
D: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
E: Mitogen-activated protein kinase 14
F: Mitogen-activated protein kinase 14
G: Mitogen-activated protein kinase 14
H: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,38324
Polymers384,7928
Non-polymers2,59116
Water75742
1
A: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
H: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8296
Polymers96,1982
Non-polymers6314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
E: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8636
Polymers96,1982
Non-polymers6654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
F: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8636
Polymers96,1982
Non-polymers6654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
G: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8296
Polymers96,1982
Non-polymers6314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.879, 107.632, 144.204
Angle α, β, γ (deg.)89.26, 76.75, 84.28
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 / Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase ...Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase 1-binding protein 1 / TAK1-binding protein 1


Mass: 54699.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAB1, MAP3K7IP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15750
#2: Protein
Mitogen-activated protein kinase 14 / MAPK 14 / CRK1 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha


Mass: 41498.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli (E. coli)
References: UniProt: P47811, mitogen-activated protein kinase

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Non-polymers , 4 types, 58 molecules

#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350, 0.1M magensium chloride, 0.1M magnesium sulphate, 0.1M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.928 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.6→140.36 Å / Num. obs: 109491 / % possible obs: 91.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 51.1 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.084 / Net I/σ(I): 7.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5166 / CC1/2: 0.413 / Rpim(I) all: 0.637 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→140.359 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.24 / Phase error: 27.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 5455 5.01 %Random selection
Rwork0.2187 ---
obs0.2213 108839 90.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→140.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21835 0 136 42 22013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122463
X-RAY DIFFRACTIONf_angle_d1.22630635
X-RAY DIFFRACTIONf_dihedral_angle_d21.0117990
X-RAY DIFFRACTIONf_chiral_restr0.0573519
X-RAY DIFFRACTIONf_plane_restr0.0083973

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