+Open data
-Basic information
Entry | Database: PDB / ID: 6nuf | |||||||||
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Title | Structure of Calcineurin in complex with NHE1 peptide | |||||||||
Components |
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Keywords | HYDROLASE/Calcium Binding Protein / Ser/thr phosphatase / complex / HYDROLASE / HYDROLASE-Calcium Binding Protein complex | |||||||||
Function / homology | Function and homology information negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / Sodium/Proton exchangers / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / protein serine/threonine phosphatase complex ...negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / Sodium/Proton exchangers / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / protein serine/threonine phosphatase complex / negative regulation of signaling / positive regulation of saliva secretion / regulation of the force of heart contraction by cardiac conduction / positive regulation of cardiac muscle hypertrophy in response to stress / positive regulation of calcium:sodium antiporter activity / positive regulation of calcium ion import across plasma membrane / Hyaluronan uptake and degradation / calmodulin-dependent protein phosphatase activity / slit diaphragm / regulation of cardiac muscle cell membrane potential / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / potassium:proton antiporter activity / cellular response to electrical stimulus / sodium:proton antiporter activity / peptidyl-serine dephosphorylation / positive regulation of action potential / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / renal filtration / skeletal muscle tissue regeneration / regulation of synaptic vesicle cycle / sodium ion export across plasma membrane / maintenance of cell polarity / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / transition between fast and slow fiber / cardiac muscle cell differentiation / cellular response to acidic pH / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / protein phosphatase 2B binding / ion binding / regulation of stress fiber assembly / cardiac muscle cell contraction / cardiac muscle hypertrophy in response to stress / response to acidic pH / positive regulation of osteoclast differentiation / regulation of cardiac muscle contraction by calcium ion signaling / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of mitochondrial membrane permeability / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / cellular response to cold / cellular response to antibiotic / cyclosporin A binding / regulation of focal adhesion assembly / myosin phosphatase activity / branching involved in blood vessel morphogenesis / protein serine/threonine phosphatase activity / CLEC7A (Dectin-1) induces NFAT activation / extrinsic component of plasma membrane / postsynaptic modulation of chemical synaptic transmission / protein-serine/threonine phosphatase / positive regulation of activated T cell proliferation / positive regulation of cardiac muscle hypertrophy / positive regulation of endocytosis / positive regulation of the force of heart contraction / Calcineurin activates NFAT / DARPP-32 events / positive regulation of cell adhesion / intercalated disc / negative regulation of insulin secretion / Activation of BAD and translocation to mitochondria / epithelial to mesenchymal transition / epidermis development / multicellular organismal response to stress / phosphatase binding / positive regulation of osteoblast differentiation / skeletal muscle fiber development / monoatomic ion transport / dephosphorylation / keratinocyte differentiation / potassium ion transmembrane transport / cellular response to epinephrine stimulus / response to amphetamine / T-tubule / excitatory postsynaptic potential / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / response to muscle stretch / proton transmembrane transport / T cell activation / FCERI mediated Ca+2 mobilization / protein dephosphorylation / stem cell differentiation / regulation of intracellular pH Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Wang, X. / Page, R. / Peti, W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: Molecular basis for the binding and selective dephosphorylation of Na+/H+exchanger 1 by calcineurin. Authors: Hendus-Altenburger, R. / Wang, X. / Sjogaard-Frich, L.M. / Pedraz-Cuesta, E. / Sheftic, S.R. / Bendsoe, A.H. / Page, R. / Kragelund, B.B. / Pedersen, S.F. / Peti, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nuf.cif.gz | 231.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nuf.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 6nuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/6nuf ftp://data.pdbj.org/pub/pdb/validation_reports/nu/6nuf | HTTPS FTP |
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-Related structure data
Related structure data | 6nucC 6nuuC 5sveS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 42855.047 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 |
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#2: Protein | Mass: 17755.174 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 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 5095.776 Da / Num. of mol.: 1 / Mutation: R698A, R700A 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 , 8 types, 482 molecules
#4: Chemical | ChemComp-FE / | ||||||||
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#5: Chemical | ChemComp-ZN / | ||||||||
#6: Chemical | ChemComp-PO4 / | ||||||||
#7: Chemical | #8: Chemical | ChemComp-PEG / | #9: Chemical | ChemComp-NA / | #10: Chemical | ChemComp-CA / #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 40% (v/v) PEG 600, 100 mM CHES/ Sodium hydroxide pH 9.5, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Oct 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→16.13 Å / Num. obs: 49574 / % possible obs: 97.6 % / Redundancy: 2.7 % / CC1/2: 0.997 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.9→1.95 Å / Num. unique obs: 5550 / CC1/2: 0.751 / % possible all: 85.59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5SVE Resolution: 1.9→16.13 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→16.13 Å
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Refine LS restraints |
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LS refinement shell |
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