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- PDB-9nxf: Crystal structure of CN:Tak1 complex -

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Basic information

Entry
Database: PDB / ID: 9nxf
TitleCrystal structure of CN:Tak1 complex
Components
  • Calcineurin subunit B type 1
  • IkB-like protein,Mitogen-activated protein kinase kinase kinase 7
  • Protein phosphatase 3 catalytic subunit alpha
KeywordsHYDROLASE / CN:TAK1 / CN / TAK1 HYDROLASE / HYDROLASE-SUBSTRATE complex
Function / homology
Function and homology information


negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / histone kinase activity / positive regulation of saliva secretion / protein serine/threonine phosphatase inhibitor activity ...negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / histone kinase activity / positive regulation of saliva secretion / protein serine/threonine phosphatase inhibitor activity / calmodulin-dependent protein phosphatase activity / I-kappaB phosphorylation / calcineurin-NFAT signaling cascade / calcineurin complex / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of JUN kinase activity / linear polyubiquitin binding / positive regulation of connective tissue replacement / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / interleukin-17A-mediated signaling pathway / positive regulation of calcium ion import across plasma membrane / MAP kinase kinase kinase kinase activity / mitogen-activated protein kinase kinase kinase / renal filtration / positive regulation of cardiac muscle hypertrophy in response to stress / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / positive regulation of calcineurin-NFAT signaling cascade / type II transforming growth factor beta receptor binding / TRIF-dependent toll-like receptor signaling pathway / skeletal muscle tissue regeneration / positive regulation of cGAS/STING signaling pathway / positive regulation of osteoclast differentiation / ATAC complex / positive regulation of vascular associated smooth muscle cell migration / anoikis / dephosphorylation / positive regulation of activated T cell proliferation / regulation of synaptic vesicle cycle / interleukin-1-mediated signaling pathway / toll-like receptor 4 signaling pathway / protein dephosphorylation / extrinsic component of plasma membrane / MyD88-dependent toll-like receptor signaling pathway / protein-serine/threonine phosphatase / regulation of postsynaptic neurotransmitter receptor internalization / stimulatory C-type lectin receptor signaling pathway / CLEC7A (Dectin-1) induces NFAT activation / epidermis development / p38MAPK cascade / Fc-epsilon receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of osteoblast differentiation / protein serine/threonine phosphatase activity / cellular response to angiotensin / parallel fiber to Purkinje cell synapse / positive regulation of macroautophagy / calcineurin-mediated signaling / positive regulation of cell size / keratinocyte differentiation / MAP kinase activity / regulation of MAPK cascade / Calcineurin activates NFAT / Activation of BAD and translocation to mitochondria / MAP kinase kinase kinase activity / DARPP-32 events / stress-activated MAPK cascade / JNK cascade / positive regulation of endocytosis / postsynaptic modulation of chemical synaptic transmission / phosphatase binding / skeletal muscle fiber development / positive regulation of vascular associated smooth muscle cell proliferation / canonical NF-kappaB signal transduction / positive regulation of interleukin-2 production / signal transduction in response to DNA damage / transforming growth factor beta receptor signaling pathway / positive regulation of cell cycle / FCERI mediated Ca+2 mobilization / positive regulation of cell adhesion / 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 / hippocampal mossy fiber to CA3 synapse / wound healing / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / protein serine/threonine kinase binding / T cell activation / TNFR1-induced NF-kappa-B signaling pathway / activated TAK1 mediates p38 MAPK activation / cellular response to tumor necrosis factor / response to calcium ion / positive regulation of T cell cytokine production / Activation of NF-kappaB in B cells / NOD1/2 Signaling Pathway / positive regulation of non-canonical NF-kappaB signal transduction / sarcolemma / TAK1-dependent IKK and NF-kappa-B activation
Similarity search - Function
: / MAP3K7 C-terminal coiled coil / PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like ...: / MAP3K7 C-terminal coiled coil / PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / EF-hand domain pair / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
: / DI(HYDROXYETHYL)ETHER / IkB-like protein / Mitogen-activated protein kinase kinase kinase 7 / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsShirakawa, K.T. / Parikh, T. / Page, R. / Peti, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144379 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01NS124666 United States
CitationJournal: Nat Commun / Year: 2026
Title: The clinical missense variant E282K in PPP3CA/calcineurin shifts substrate dephosphorylation by altering active site recruitment.
Authors: Shirakawa, K.T. / Parikh, T. / Machado, L.E.S.F. / Poimenidou, G. / Nguyen, H.T. / Dell'Acqua, M.L. / Kettenbach, A.N. / Page, R. / Peti, W.
History
DepositionMar 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein phosphatase 3 catalytic subunit alpha
B: Calcineurin subunit B type 1
C: IkB-like protein,Mitogen-activated protein kinase kinase kinase 7
D: Protein phosphatase 3 catalytic subunit alpha
E: Calcineurin subunit B type 1
F: IkB-like protein,Mitogen-activated protein kinase kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,12720
Polymers133,2846
Non-polymers84314
Water37821
1
A: Protein phosphatase 3 catalytic subunit alpha
B: Calcineurin subunit B type 1
C: IkB-like protein,Mitogen-activated protein kinase kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,07110
Polymers66,6423
Non-polymers4287
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-92 kcal/mol
Surface area23970 Å2
MethodPISA
2
D: Protein phosphatase 3 catalytic subunit alpha
E: Calcineurin subunit B type 1
F: IkB-like protein,Mitogen-activated protein kinase kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,05710
Polymers66,6423
Non-polymers4147
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-103 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.079, 49.585, 158.895
Angle α, β, γ (deg.)90.000, 128.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Protein phosphatase 3 catalytic subunit alpha / CAM-PRP catalytic subunit / Calcineurin A alpha / Calmodulin-dependent calcineurin A subunit alpha ...CAM-PRP catalytic subunit / Calcineurin A alpha / Calmodulin-dependent calcineurin A subunit alpha isoform / CNA alpha / Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform


Mass: 42615.840 Da / Num. of mol.: 2 / Mutation: D90A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Production host: Escherichia coli (E. coli)
References: UniProt: Q08209, protein-serine/threonine phosphatase
#2: Protein Calcineurin subunit B type 1 / Protein phosphatase 2B regulatory subunit 1 / Protein phosphatase 3 regulatory subunit B alpha isoform 1


Mass: 17755.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: sequence 15-170 / Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1, CNA2, CNB / Production host: Escherichia coli (E. coli) / References: UniProt: P63098
#3: Protein IkB-like protein,Mitogen-activated protein kinase kinase kinase 7 / Ankyrin repeat domain-containing protein A238L / p28 / Transforming growth factor-beta-activated ...Ankyrin repeat domain-containing protein A238L / p28 / Transforming growth factor-beta-activated kinase 1 / TGF-beta-activated kinase 1


Mass: 6271.200 Da / Num. of mol.: 2 / Mutation: Q441R,D442P
Source method: isolated from a genetically manipulated source
Details: A238L-TAK1 chimera, A238L 200-228 and TAK1 422-442 (Q441R, D442P)
Source: (gene. exp.) Homo sapiens (human) / Gene: A238L, Mal-047, 5EL, MAP3K7, TAK1 / Production host: Escherichia coli (E. coli)
References: UniProt: O36972, UniProt: O43318, mitogen-activated protein kinase kinase kinase

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Non-polymers , 5 types, 35 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.58 Å3/Da / Density % sol: 52.39 % / Description: Long plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 200 mM Sodium citrate tribasic pH 8.4, 22% PEG 3350, 3% ethanol. Microseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 3.13→34.94 Å / Num. obs: 23625 / % possible obs: 96 % / Redundancy: 6.8 % / Biso Wilson estimate: 51.81 Å2 / CC1/2: 0.935 / Net I/σ(I): 3.5
Reflection shellResolution: 3.13→3.184 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1213 / CC1/2: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.13→34.94 Å / SU ML: 0.4708 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.4234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2954 1179 5 %
Rwork0.2479 22394 -
obs0.2503 23573 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.39 Å2
Refinement stepCycle: LAST / Resolution: 3.13→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8726 0 37 21 8784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00148956
X-RAY DIFFRACTIONf_angle_d0.399912094
X-RAY DIFFRACTIONf_chiral_restr0.03781305
X-RAY DIFFRACTIONf_plane_restr0.00311576
X-RAY DIFFRACTIONf_dihedral_angle_d10.5583355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.270.35241250.27392902X-RAY DIFFRACTION99.21
3.27-3.440.33871580.26672865X-RAY DIFFRACTION99.8
3.44-3.630.33231360.27042566X-RAY DIFFRACTION99.96
3.68-3.940.30331220.26322252X-RAY DIFFRACTION83.24
3.94-4.340.2961730.232891X-RAY DIFFRACTION99.93
4.34-4.960.24921500.20582938X-RAY DIFFRACTION99.81
4.96-6.250.2671470.26152961X-RAY DIFFRACTION99.9
6.25-34.940.29041680.25073019X-RAY DIFFRACTION99.75

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