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- PDB-2pzf: Minimal human CFTR first nucleotide binding domain as a head-to-t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pzf | ||||||
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Title | Minimal human CFTR first nucleotide binding domain as a head-to-tail dimer with delta F508 | ||||||
![]() | Cystic fibrosis transmembrane conductance regulator | ||||||
![]() | HYDROLASE / NBD / ABC transporter / CFTR / F508 | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Atwell, S. / Conners, K. / Emtage, S. / Gheyi, T. / Glenn, N.R. / Hendle, J. / Lewis, H.A. / Lu, F. / Rodgers, L.A. / Romero, R. ...Atwell, S. / Conners, K. / Emtage, S. / Gheyi, T. / Glenn, N.R. / Hendle, J. / Lewis, H.A. / Lu, F. / Rodgers, L.A. / Romero, R. / Sauder, J.M. / Smith, D. / Tien, H. / Wasserman, S.R. / Zhao, X. | ||||||
![]() | ![]() Title: Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant. Authors: Atwell, S. / Brouillette, C.G. / Conners, K. / Emtage, S. / Gheyi, T. / Guggino, W.B. / Hendle, J. / Hunt, J.F. / Lewis, H.A. / Lu, F. / Protasevich, I.I. / Rodgers, L.A. / Romero, R. / ...Authors: Atwell, S. / Brouillette, C.G. / Conners, K. / Emtage, S. / Gheyi, T. / Guggino, W.B. / Hendle, J. / Hunt, J.F. / Lewis, H.A. / Lu, F. / Protasevich, I.I. / Rodgers, L.A. / Romero, R. / Wasserman, S.R. / Weber, P.C. / Wetmore, D. / Zhang, F.F. / Zhao, X. #1: Journal: Pediatr.Pulmonol.Suppl. / Year: 2007 Title: Structure of the human CFTR NBD1 domain as a homodimer: insights and applications Authors: Atwell, S. / Conners, K. / Emtage, S. / Gheyi, T. / Lewis, H. / Lu, F. / Romero, R. / Zhao, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.2 KB | Display | ![]() |
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PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pzeSC ![]() 2pzgC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components
#1: Protein | Mass: 25378.232 Da / Num. of mol.: 2 / Fragment: CFTR NBD1 387-646 / Mutation: del405-436, delF508 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion / pH: 8.5 Details: Protein: 9.5mg/ml NBD1, 0.15M NaCl, 0.01M methionine, 0.01M HEPES pH 7.5, 10% glycerol, 0.001M TCEP, 0.002M ATP; Well: 0.1M Tris pH 8.5, 35% PEG 4K, 0.2M NaAcetate; Cryo: 25% DMSO, vapor ...Details: Protein: 9.5mg/ml NBD1, 0.15M NaCl, 0.01M methionine, 0.01M HEPES pH 7.5, 10% glycerol, 0.001M TCEP, 0.002M ATP; Well: 0.1M Tris pH 8.5, 35% PEG 4K, 0.2M NaAcetate; Cryo: 25% DMSO, vapor diffusion, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2007 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→25.583 Å / Num. all: 29245 / Num. obs: 29245 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 4.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PZE Resolution: 2→25.118 Å / Isotropic thermal model: isotropic / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: Mask bulk solvent correction | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.015 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.118 Å
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Refine LS restraints |
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