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- PDB-5tf8: Nucleotide-binding domain 1 of the human cystic fibrosis transmem... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tf8 | ||||||
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Title | Nucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with dTTP | ||||||
![]() | Cystic fibrosis transmembrane conductance regulator | ||||||
![]() | HYDROLASE / hNBD1 / CFTR / ABC transport / ATP | ||||||
Function / homology | ![]() positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / amelogenesis ...positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / amelogenesis / chloride channel inhibitor activity / ATPase-coupled inorganic anion transmembrane transporter activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / membrane hyperpolarization / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / vesicle docking involved in exocytosis / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / RHOQ GTPase cycle / cholesterol biosynthetic process / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / cellular response to cAMP / cellular response to forskolin / chloride transmembrane transport / isomerase activity / response to endoplasmic reticulum stress / establishment of localization in cell / PDZ domain binding / Defective CFTR causes cystic fibrosis / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ABC-family proteins mediated transport / recycling endosome / transmembrane transport / Aggrephagy / Chaperone Mediated Autophagy / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / protein-folding chaperone binding / early endosome / endosome membrane / Ub-specific processing proteases / apical plasma membrane / lysosomal membrane / endoplasmic reticulum membrane / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, C. / Aleksandrov, A.A. / Yang, Z. / Forouhar, F. / Proctor, E. / Kota, P. / An, J. / Kaplan, A. / Khazanov, N. / Boel, G. ...Wang, C. / Aleksandrov, A.A. / Yang, Z. / Forouhar, F. / Proctor, E. / Kota, P. / An, J. / Kaplan, A. / Khazanov, N. / Boel, G. / Stockwell, B.R. / Senderowitz, H. / Dokholyan, N.V. / Riordan, J.R. / Brouillette, C.G. / Hunt, J.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Thermodynamic correction of F508del-CFTR by ligand binding to a remote site in the mutated domain Authors: Wang, C. / Aleksandrov, A.A. / Yang, Z. / Forouhar, F. / Proctor, E. / Kota, P. / An, J. / Kaplan, A. / Khazanov, N. / Boel, G. / Stockwell, B.R. / Senderowitz, H. / Dokholyan, N.V. / ...Authors: Wang, C. / Aleksandrov, A.A. / Yang, Z. / Forouhar, F. / Proctor, E. / Kota, P. / An, J. / Kaplan, A. / Khazanov, N. / Boel, G. / Stockwell, B.R. / Senderowitz, H. / Dokholyan, N.V. / Riordan, J.R. / Brouillette, C.G. / Hunt, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.7 KB | Display | ![]() |
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PDB format | ![]() | 46 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 745.9 KB | Display | ![]() |
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Full document | ![]() | 747.3 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tf7C ![]() 5tfaC ![]() 5tfbC ![]() 5tfcC ![]() 5tfdC ![]() 5tffC ![]() 5tfgC ![]() 5tfiC ![]() 5tfjC ![]() 2pzeS ![]() 5tfe ![]() 5tfh C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25525.408 Da / Num. of mol.: 1 Fragment: Nucleotide-binding domain 1 (UNP residues 387-646) Mutation: V470M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P13569, EC: 3.6.3.49 |
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#2: Chemical | ChemComp-TTP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.66 % |
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Crystal grow | Temperature: 279 K / Method: microbatch / pH: 7.5 Details: Protein buffer:containing 150 mM NaCl, 30% (v/v) glycerol, 1 mM TCEP, and 20 mM Na-HEPES, pH 7.5, Precipitant buffer: 40% (v/v) PEG 400, 100 mM NH4Cl, and 100 mM MES, pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 18715 / % possible obs: 99.5 % / Redundancy: 3.9 % / Net I/σ(I): 31.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2pze Resolution: 1.861→40.188 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 17.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.861→40.188 Å
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Refine LS restraints |
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LS refinement shell |
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