+Open data
-Basic information
Entry | Database: PDB / ID: 9b9g | |||||||||
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Title | Structure of the PI4KA complex bound to Calcineurin | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / PI4KIIIa complex / PI4KA / TTC7B / FAM126A / CNA / CNB / Calcineurin | |||||||||
Function / homology | Function and homology information reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of cardiac muscle hypertrophy in response to stress / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling ...reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of cardiac muscle hypertrophy in response to stress / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling / positive regulation of saliva secretion / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / calmodulin-dependent protein phosphatase activity / positive regulation of calcium ion import across plasma membrane / calcineurin complex / positive regulation of connective tissue replacement / calcineurin-mediated signaling / negative regulation of dendrite morphogenesis / slit diaphragm / protein serine/threonine phosphatase complex / peptidyl-serine dephosphorylation / modulation by host of viral process / Synthesis of PIPs at the Golgi membrane / renal filtration / transition between fast and slow fiber / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / skeletal muscle tissue regeneration / regulation of synaptic vesicle cycle / Golgi-associated vesicle membrane / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / phosphatidylinositol biosynthetic process / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / CLEC7A (Dectin-1) induces NFAT activation / myosin phosphatase activity / extrinsic component of plasma membrane / protein serine/threonine phosphatase activity / postsynaptic modulation of chemical synaptic transmission / cyclosporin A binding / branching involved in blood vessel morphogenesis / protein-serine/threonine phosphatase / dephosphorylation / positive regulation of activated T cell proliferation / phosphatidylinositol-mediated signaling / positive regulation of endocytosis / phosphatidylinositol phosphate biosynthetic process / Calcineurin activates NFAT / DARPP-32 events / epidermis development / Activation of BAD and translocation to mitochondria / epithelial to mesenchymal transition / phosphatase binding / negative regulation of insulin secretion / positive regulation of osteoblast differentiation / multicellular organismal response to stress / skeletal muscle fiber development / keratinocyte differentiation / phosphorylation / myelination / response to amphetamine / protein dephosphorylation / hippocampal mossy fiber to CA3 synapse / positive regulation of cell adhesion / FCERI mediated Ca+2 mobilization / T cell activation / excitatory postsynaptic potential / protein localization to plasma membrane / cellular response to glucose stimulus / wound healing / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / sarcolemma / Z disc / response to calcium ion / protein import into nucleus / G1/S transition of mitotic cell cycle / calcium ion transport / kinase activity / heart development / Ca2+ pathway / ATPase binding / postsynapse / dendritic spine / protein dimerization activity / calmodulin binding / positive regulation of cell migration / neuron projection / cadherin binding / protein domain specific binding / negative regulation of gene expression / focal adhesion / glutamatergic synapse / calcium ion binding / protein-containing complex binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Shaw, A.L. / Suresh, S. / Yip, C.K. / Burke, J.E. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Structure / Year: 2024 Title: Structure of calcineurin bound to PI4KA reveals dual interface in both PI4KA and FAM126A. Authors: Alexandria L Shaw / Sushant Suresh / Matthew A H Parson / Noah J Harris / Meredith L Jenkins / Calvin K Yip / John E Burke / Abstract: Phosphatidylinositol 4-kinase alpha (PI4KA) maintains the phosphatidylinositol 4-phosphate (PI4P) and phosphatidylserine pools of the plasma membrane. A key regulator of PI4KA is its association into ...Phosphatidylinositol 4-kinase alpha (PI4KA) maintains the phosphatidylinositol 4-phosphate (PI4P) and phosphatidylserine pools of the plasma membrane. A key regulator of PI4KA is its association into a complex with TTC7 and FAM126 proteins. This complex can be regulated by the CNAβ1 isoform of the phosphatase calcineurin. We previously identified that CNAβ1 directly binds to FAM126A. Here, we report a cryoelectron microscopic (cryo-EM) structure of a truncated PI4KA complex bound to calcineurin, revealing a unique direct interaction between PI4KA and calcineurin. Hydrogen deuterium exchange mass spectrometry (HDX-MS) and computational analysis show that calcineurin forms a complex with an evolutionarily conserved IKISVT sequence in PI4KA's horn domain. We also characterized conserved LTLT and PSISIT calcineurin binding sequences in the C terminus of FAM126A. These dual sites in PI4KA and FAM126A are both in close proximity to phosphorylation sites in the PI4KA complex, suggesting key roles of calcineurin-regulated phosphosites in PI4KA regulation. This work reveals novel insight into how calcineurin can regulate PI4KA activity. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9b9g.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9b9g.ent.gz | 878.2 KB | Display | PDB format |
PDBx/mmJSON format | 9b9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b9g_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 9b9g_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 9b9g_validation.xml.gz | 169.5 KB | Display | |
Data in CIF | 9b9g_validation.cif.gz | 257.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/9b9g ftp://data.pdbj.org/pub/pdb/validation_reports/b9/9b9g | HTTPS FTP |
-Related structure data
Related structure data | 44382MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 10 molecules ABDFEGHJIK
#1: Protein | Mass: 237102.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KA, PIK4, PIK4CA / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P42356, 1-phosphatidylinositol 4-kinase #2: Protein | Mass: 94294.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTC7B, TTC7L1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86TV6 #3: Protein | Mass: 34638.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Truncated construct (1-308) / Source: (gene. exp.) Homo sapiens (human) / Gene: HYCC1, DRCTNNB1A, FAM126A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BYI3 #4: Protein | Mass: 19322.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1, CNA2, CNB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P63098 #5: Protein | Mass: 70883.242 Da / Num. of mol.: 2 / Mutation: L236P,D238N Source method: isolated from a genetically manipulated source Details: Truncated Calcineurin A alpha (2-391) L236P D238N,Truncated Calcineurin A alpha (2-391) L236P D238N Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: Q08209, protein-serine/threonine phosphatase |
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-Non-polymers , 1 types, 8 molecules
#6: Chemical | ChemComp-CA / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PI4KA complex bound to Calcineurin / Type: COMPLEX / Details: Stabilized with BS3 crosslinker / Entity ID: #1-#5 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | |||||||||||||||||||||||||
Buffer solution | pH: 7 Details: Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.77 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Sample was treated with BS3 crosslinker then gel filtered to isolate protein peak consistent with a dimer of pentamers. | |||||||||||||||||||||||||
Specimen support | Details: Glow discharged using the Pelco EasiGlow. 15mA Current. Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Blot force -5, blot time 1 s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10121 |
EM imaging optics | Energyfilter name: TFS Selectris |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1181312 Details: Particles were picked using the cryoSPARC template picker | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 235760 / Symmetry type: POINT | ||||||||||||||||||||||||
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