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- PDB-2jog: Structure of the calcineurin-NFAT complex -

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Basic information

Entry
Database: PDB / ID: 2jog
TitleStructure of the calcineurin-NFAT complex
Components
  • Calmodulin-dependent calcineurin A subunit alpha isoform
  • NFAT
KeywordsHYDROLASE / calcineurin / NFAT / complex structure / phosphatase
Function / homology
Function and homology information


negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / protein serine/threonine phosphatase complex / negative regulation of signaling / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity ...negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / protein serine/threonine phosphatase complex / negative regulation of signaling / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / slit diaphragm / peptidyl-serine dephosphorylation / calcineurin-NFAT signaling cascade / renal filtration / skeletal muscle tissue regeneration / transition between fast and slow fiber / positive regulation of calcineurin-NFAT signaling cascade / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / dendrite morphogenesis / cyclosporin A binding / myosin phosphatase activity / CLEC7A (Dectin-1) induces NFAT activation / postsynaptic modulation of chemical synaptic transmission / extrinsic component of plasma membrane / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of activated T cell proliferation / positive regulation of endocytosis / Calcineurin activates NFAT / positive regulation of cell adhesion / DARPP-32 events / epidermis development / negative regulation of insulin secretion / multicellular organismal response to stress / positive regulation of osteoblast differentiation / skeletal muscle fiber development / dephosphorylation / keratinocyte differentiation / response to amphetamine / T cell activation / excitatory postsynaptic potential / FCERI mediated Ca+2 mobilization / protein dephosphorylation / cellular response to glucose stimulus / wound healing / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / sarcolemma / Z disc / response to calcium ion / G1/S transition of mitotic cell cycle / protein import into nucleus / calcium ion transport / Ca2+ pathway / ATPase binding / dendritic spine / protein dimerization activity / calmodulin binding / positive regulation of cell migration / negative regulation of gene expression / glutamatergic synapse / calcium ion binding / positive regulation of gene expression / protein-containing complex binding / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like ...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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTakeuchi, K. / Roehrl, M.H. / Sun, Z.Y. / Wagner, G.
CitationJournal: Structure / Year: 2007
Title: Structure of the Calcineurin-NFAT Complex: Defining a T Cell Activation Switch Using Solution NMR and Crystal Coordinates.
Authors: Takeuchi, K. / Roehrl, M.H. / Sun, Z.Y. / Wagner, G.
History
DepositionMar 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-dependent calcineurin A subunit alpha isoform
B: NFAT


Theoretical massNumber of molelcules
Total (without water)39,5922
Polymers39,5922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 37866.309 Da / Num. of mol.: 1 / Fragment: residues 21-347
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/peptide NFAT


Mass: 1725.937 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The author states that this is an artificial sequence based on the NFAT sequences. The reference for the NFAT sequences is Aramburu, J., Yaffe, M. B., Lopez-Rodriguez, C., Cantley, L.C., ...Details: The author states that this is an artificial sequence based on the NFAT sequences. The reference for the NFAT sequences is Aramburu, J., Yaffe, M. B., Lopez-Rodriguez, C., Cantley, L.C., Hogan, P.G., and Rao, A. (1999). Affinity-driven peptide selection of an NFAT inhibitor more selective than cyclosporin A. Science 285, 2129-2133.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D 1H-15N NOESY
1512D 1H-1H NOESY
1622D 1H-15N HSQC
1723D HNCA
1823D HN(CA)CB
1923D 1H-15N TOCSY
11032D 1H-13C HSQC
11133D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1500uM [U-13C; U-15N; U-2H] calcineurin, 0.4-0.6 mM NFAT, 90% H2O/10% D2O90% H2O/10% D2O
2300uM calcineurin, 0.3 mM [U-13C; U-15N; U-2H] NFAT, 90% H2O/10% D2O90% H2O/10% D2O
3400uM [2H, FIMY-1H] calcineurin, 0.4 mM [ul-2H15N, Id1LdVg -1H13C] NFAT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMentity_1[U-13C; U-15N; U-2H]1
0.4 mMentity_21
0.3 mMentity_12
0.3 mMentity_2[U-13C; U-15N; U-2H]2
0.4 mMentity_1[2H, FIMY-1H]3
0.4 mMentity_2[ul-2H15N, Id1LdVg -1H13C]3
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddarddata analysis
XwinNMRBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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