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- PDB-9nxe: Crystal Structure of Calcineurin Clinical Variant E282K -

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Basic information

Entry
Database: PDB / ID: 9nxe
TitleCrystal Structure of Calcineurin Clinical Variant E282K
Components
  • Calcineurin subunit B type 1
  • Protein phosphatase 3 catalytic subunit alpha
  • Sodium/hydrogen exchanger 1
KeywordsHYDROLASE / CN E282K / CN / clinical variant
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 / regulation of the force of heart contraction by cardiac conduction / Sodium/Proton exchangers / 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 / positive regulation of saliva secretion ...negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / regulation of the force of heart contraction by cardiac conduction / Sodium/Proton exchangers / 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 / positive regulation of saliva secretion / calmodulin-dependent protein phosphatase activity / calcineurin-NFAT signaling cascade / Hyaluronan degradation / calcineurin complex / cation-transporting ATPase complex / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / positive regulation of connective tissue replacement / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion import across plasma membrane / renal filtration / positive regulation of cardiac muscle hypertrophy in response to stress / potassium:proton antiporter activity / regulation of pH / positive regulation of action potential / hyaluronan catabolic process / maintenance of cell polarity / sodium:proton antiporter activity / positive regulation of calcineurin-NFAT signaling cascade / sodium ion export across plasma membrane / skeletal muscle tissue regeneration / intracellular sodium ion homeostasis / protein phosphatase 2B binding / regulation of stress fiber assembly / positive regulation of osteoclast differentiation / positive regulation of mitochondrial membrane permeability / response to acidic pH / dephosphorylation / positive regulation of activated T cell proliferation / regulation of synaptic vesicle cycle / sodium ion import across plasma membrane / regulation of cardiac muscle contraction by calcium ion signaling / regulation of focal adhesion assembly / protein dephosphorylation / extrinsic component of plasma membrane / cardiac muscle cell contraction / cellular response to cold / positive regulation of cardiac muscle hypertrophy / protein-serine/threonine phosphatase / cellular response to antibiotic / regulation of postsynaptic neurotransmitter receptor internalization / CLEC7A (Dectin-1) induces NFAT activation / epidermis development / positive regulation of the force of heart contraction / positive regulation of osteoblast differentiation / protein complex oligomerization / protein serine/threonine phosphatase activity / parallel fiber to Purkinje cell synapse / calcineurin-mediated signaling / keratinocyte differentiation / intercalated disc / Calcineurin activates NFAT / Activation of BAD and translocation to mitochondria / DARPP-32 events / positive regulation of endocytosis / response to muscle stretch / postsynaptic modulation of chemical synaptic transmission / phosphatase binding / skeletal muscle fiber development / cellular response to acidic pH / phosphatidylinositol-4,5-bisphosphate binding / cellular response to epinephrine stimulus / FCERI mediated Ca+2 mobilization / potassium ion transmembrane transport / proton transmembrane transport / positive regulation of cell adhesion / T-tubule / hippocampal mossy fiber to CA3 synapse / wound healing / regulation of intracellular pH / T cell activation / sodium ion transmembrane transport / cellular response to mechanical stimulus / response to calcium ion / sarcolemma / phospholipid binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / Z disc / calcium-dependent protein binding / cellular response to insulin stimulus / cell migration / positive regulation of cell growth / lamellipodium / ATPase binding / cellular response to hypoxia / Ca2+ pathway / molecular adaptor activity / dendritic spine / basolateral plasma membrane
Similarity search - Function
Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / PP2B, metallophosphatase domain / PP2B / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / Serine/threonine specific protein phosphatases signature. ...Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / PP2B, metallophosphatase domain / PP2B / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / 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 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Sodium/hydrogen exchanger 1 / 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: 2.09 Å
AuthorsParikh, T. / Shirakawa, K.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

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Assembly

Deposited unit
A: Protein phosphatase 3 catalytic subunit alpha
B: Calcineurin subunit B type 1
C: Sodium/hydrogen exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,07110
Polymers65,6833
Non-polymers3887
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-115 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.490, 126.501, 127.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-640-

HOH

31A-661-

HOH

41A-664-

HOH

51A-675-

HOH

61A-677-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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: 42659.918 Da / Num. of mol.: 1 / Mutation: E282K
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.: 1
Source method: isolated from a genetically manipulated source
Details: CNB 15-170 / Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1, CNA2, CNB / Production host: Escherichia coli (E. coli) / References: UniProt: P63098

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Sodium/hydrogen exchanger 1 / APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute ...APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1


Mass: 5268.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A1, APNH1, NHE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19634

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Non-polymers , 5 types, 240 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M CAPS pH 9, 0.2 M MgCl2 and 24% PEG 600

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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: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.089→67.305 Å / Num. obs: 38378 / % possible obs: 99.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 37.75 Å2 / CC1/2: 0.994 / Net I/σ(I): 5.5
Reflection shellResolution: 2.089→2.125 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1888 / CC1/2: 0.351 / % possible all: 99.6

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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: 2.09→37.95 Å / SU ML: 0.353 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 1763 4.63 %
Rwork0.2023 36315 -
obs0.2042 38078 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.3 Å2
Refinement stepCycle: LAST / Resolution: 2.09→37.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 13 233 4460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274327
X-RAY DIFFRACTIONf_angle_d0.48385855
X-RAY DIFFRACTIONf_chiral_restr0.0396638
X-RAY DIFFRACTIONf_plane_restr0.0038765
X-RAY DIFFRACTIONf_dihedral_angle_d11.11771607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.38091270.372630X-RAY DIFFRACTION93.74
2.15-2.210.41831310.34472711X-RAY DIFFRACTION97.36
2.21-2.280.32611310.31662748X-RAY DIFFRACTION98.97
2.28-2.360.38291270.29022781X-RAY DIFFRACTION99.69
2.36-2.460.31431390.27132800X-RAY DIFFRACTION99.83
2.46-2.570.28591420.24532741X-RAY DIFFRACTION98.16
2.57-2.70.28261180.23252812X-RAY DIFFRACTION99.9
2.7-2.870.29371590.21832798X-RAY DIFFRACTION99.86
2.87-3.090.25581250.21212834X-RAY DIFFRACTION99.76
3.09-3.40.22991500.19952795X-RAY DIFFRACTION99.66
3.4-3.90.2091370.17042820X-RAY DIFFRACTION99.39
3.9-4.910.17661590.14012859X-RAY DIFFRACTION99.83
4.91-37.950.21011180.16982986X-RAY DIFFRACTION99.26

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