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Yorodumi- PDB-2bec: Crystal structure of CHP2 in complex with its binding region in N... -
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-Basic information
Entry | Database: PDB / ID: 2bec | ||||||
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Title | Crystal structure of CHP2 in complex with its binding region in NHE1 and insights into the mechanism of pH regulation | ||||||
Components |
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Keywords | METAL BINDING PROTEIN/TRANSPORT PROTEIN / Calcineurin-homologous protein / Calcium-binding protein / NHE1 regulating protein / METAL BINDING PROTEIN-TRANSPORT PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / positive regulation of calcium:sodium antiporter activity / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / positive regulation of phosphatase activity / cellular response to electrical stimulus / potassium:proton antiporter activity ...sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / positive regulation of calcium:sodium antiporter activity / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / positive regulation of phosphatase activity / cellular response to electrical stimulus / potassium:proton antiporter activity / sodium:proton antiporter activity / positive regulation of action potential / sodium ion export across plasma membrane / maintenance of cell polarity / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / 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 / response to acidic pH / positive regulation of mitochondrial membrane permeability / regulation of cardiac muscle contraction by calcium ion signaling / cellular response to cold / cellular response to antibiotic / regulation of focal adhesion assembly / positive regulation of cardiac muscle hypertrophy / positive regulation of the force of heart contraction / cellular response to organic cyclic compound / intercalated disc / monoatomic ion transport / potassium ion transmembrane transport / T-tubule / cellular response to epinephrine stimulus / proton transmembrane transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / response to muscle stretch / stem cell differentiation / regulation of intracellular pH / phospholipid binding / positive regulation of protein import into nucleus / cellular response to mechanical stimulus / cellular response to insulin stimulus / calcium-dependent protein binding / cell migration / protein transport / protein-macromolecule adaptor activity / lamellipodium / protein complex oligomerization / cellular response to hypoxia / positive regulation of cell growth / basolateral plasma membrane / molecular adaptor activity / calmodulin binding / membrane raft / apical plasma membrane / positive regulation of apoptotic process / focal adhesion / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Ben Ammar, Y. / Takeda, S. / Hisamitsu, T. / Mori, H. / Wakabayashi, S. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Crystal structure of CHP2 complexed with NHE1-cytosolic region and an implication for pH regulation Authors: Ben Ammar, Y. / Takeda, S. / Hisamitsu, T. / Mori, H. / Wakabayashi, S. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2005 Title: Crystallization and preliminary crystallographic analysis of the human calcineurin homologous protein CHP2 bound to the cytoplasmic region of the Na+/H+ exchanger NHE1 Authors: Ben Ammar, Y. / Takeda, S. / Sugawara, M. / Miyano, M. / Mori, H. / Wakabayashi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bec.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bec.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2bec ftp://data.pdbj.org/pub/pdb/validation_reports/be/2bec | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Asymmetric unit contains one physiological unit |
-Components
#1: Protein | Mass: 23316.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star / References: UniProt: O43745 |
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#2: Protein/peptide | Mass: 5015.683 Da / Num. of mol.: 1 / Fragment: residues 503-545 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star / References: UniProt: P19634 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.2M ammonium acetate, 0.1M Bis-Tris, 0.01M yttrium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. all: 6996 / Num. obs: 6807 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 83.1 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.7→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree: 0.514 / Rfactor Rwork: 0.385 |