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- PDB-9nxn: Crystal structure of CN:RII alpha -

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Basic information

Entry
Database: PDB / ID: 9nxn
TitleCrystal structure of CN:RII alpha
Components
  • Calcineurin subunit B type 1
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
KeywordsHYDROLASE / CN:RII alpha / CN / RII 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 / positive regulation of saliva secretion / peptidyl-serine dephosphorylation / calmodulin-dependent protein phosphatase 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 / positive regulation of saliva secretion / peptidyl-serine dephosphorylation / calmodulin-dependent protein phosphatase activity / calcineurin complex / cAMP-dependent protein kinase regulator activity / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / positive regulation of connective tissue replacement / positive regulation of calcium ion import across plasma membrane / ROBO receptors bind AKAP5 / positive regulation of cardiac muscle hypertrophy in response to stress / protein serine/threonine phosphatase complex / negative regulation of dendrite morphogenesis / renal filtration / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / nucleotide-activated protein kinase complex / positive regulation of calcineurin-NFAT signaling cascade / skeletal muscle tissue regeneration / transition between fast and slow fiber / myelination in peripheral nervous system / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / regulation of synaptic vesicle cycle / negative regulation of cAMP/PKA signal transduction / dephosphorylation / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / extrinsic component of plasma membrane / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / branching involved in blood vessel morphogenesis / CLEC7A (Dectin-1) induces NFAT activation / dendrite morphogenesis / protein-serine/threonine phosphatase / regulation of postsynaptic neurotransmitter receptor internalization / ciliary base / protein kinase A catalytic subunit binding / parallel fiber to Purkinje cell synapse / protein serine/threonine phosphatase activity / calcineurin-mediated signaling / positive regulation of activated T cell proliferation / plasma membrane raft / PKA activation in glucagon signalling / epithelial to mesenchymal transition / Calcineurin activates NFAT / positive regulation of endocytosis / DARPP-32 events / epidermis development / Activation of BAD and translocation to mitochondria / positive regulation of osteoblast differentiation / phosphatase binding / multicellular organismal response to stress / postsynaptic modulation of chemical synaptic transmission / protein dephosphorylation / cAMP binding / Hedgehog 'off' state / keratinocyte differentiation / skeletal muscle fiber development / FCERI mediated Ca+2 mobilization / positive regulation of cell adhesion / FCGR3A-mediated IL10 synthesis / T cell activation / hippocampal mossy fiber to CA3 synapse / excitatory postsynaptic potential / wound healing / G1/S transition of mitotic cell cycle / response to calcium ion / sarcolemma / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / Z disc / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein import into nucleus / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / calcium ion transport / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / heart development / Factors involved in megakaryocyte development and platelet production / ATPase binding / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / dendritic spine / calmodulin binding / postsynapse / protein dimerization activity / intracellular signal transduction / positive regulation of cell migration / protein domain specific binding / negative regulation of gene expression / focal adhesion / calcium ion binding
Similarity search - Function
PP2B, metallophosphatase domain / PP2B / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase ...PP2B, metallophosphatase domain / PP2B / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / 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
cAMP-dependent protein kinase type II-alpha regulatory subunit / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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: To Be Published
Title: CN:Tak1 complex explains CN substrate specificity
Authors: Shirakawa, K.T. / Parikh, T. / Page, R. / Peti, W.
History
DepositionMar 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
B: Calcineurin subunit B type 1
C: cAMP-dependent protein kinase type II-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0547
Polymers68,8933
Non-polymers1604
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-89 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.535, 102.982, 107.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 42659.852 Da / Num. of mol.: 1
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: 19322.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1, CNA2, CNB / Production host: Escherichia coli (E. coli) / References: UniProt: P63098
#3: Protein cAMP-dependent protein kinase type II-alpha regulatory subunit


Mass: 6910.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR2A, PKR2, PRKAR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13861
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate pH 5.0, 0.1 M Magnesium chloride hexahydrate, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2.1→21.63 Å / Num. obs: 36938 / % possible obs: 98.8 % / Redundancy: 9.5 % / Biso Wilson estimate: 8.03 Å2 / CC1/2: 0.986 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2601 / CC1/2: 0.585 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PROTEUM PLUSdata reduction
Aimless0.7.3data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→21.59 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 21.9053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 1909 5.42 %
Rwork0.2088 33339 -
obs0.2111 35248 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 4 442 4650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00134323
X-RAY DIFFRACTIONf_angle_d0.39935859
X-RAY DIFFRACTIONf_chiral_restr0.0379641
X-RAY DIFFRACTIONf_plane_restr0.0025767
X-RAY DIFFRACTIONf_dihedral_angle_d11.04211591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.30141300.26652458X-RAY DIFFRACTION99.62
2.15-2.210.30471480.25392438X-RAY DIFFRACTION99.31
2.21-2.280.30261310.23912424X-RAY DIFFRACTION99.34
2.28-2.350.27531450.2332434X-RAY DIFFRACTION98.89
2.35-2.430.27011400.22462432X-RAY DIFFRACTION98.92
2.43-2.530.28651450.22032425X-RAY DIFFRACTION97.83
2.53-2.650.26321390.21932401X-RAY DIFFRACTION97.58
2.65-2.780.23871350.2142401X-RAY DIFFRACTION96.83
2.78-2.960.26611320.21532267X-RAY DIFFRACTION92.09
2.96-3.190.27441290.22162220X-RAY DIFFRACTION89.25
3.19-3.510.25131230.20722234X-RAY DIFFRACTION89.48
3.51-4.010.20841310.16712342X-RAY DIFFRACTION92.62
4.01-5.040.16921390.15382381X-RAY DIFFRACTION93.4
5.04-21.590.21361420.18122482X-RAY DIFFRACTION93.38

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