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Yorodumi- PDB-2pze: Minimal human CFTR first nucleotide binding domain as a head-to-t... -
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-Basic information
Entry | Database: PDB / ID: 2pze | ||||||
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Title | Minimal human CFTR first nucleotide binding domain as a head-to-tail dimer | ||||||
Components | Cystic fibrosis transmembrane conductance regulator | ||||||
Keywords | HYDROLASE / NBD / ABC transporter / CFTR | ||||||
Function / homology | Function and homology information 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 / ATPase-coupled inorganic anion transmembrane transporter activity ...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 / ATPase-coupled inorganic anion transmembrane transporter activity / amelogenesis / chloride channel inhibitor activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / vesicle docking involved in exocytosis / cholesterol transport / membrane hyperpolarization / bicarbonate transmembrane transporter activity / bicarbonate transport / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / RHOQ GTPase cycle / 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 forskolin / cellular response to cAMP / isomerase activity / chloride transmembrane transport / response to endoplasmic reticulum stress / PDZ domain binding / establishment of localization in cell / Defective CFTR causes cystic fibrosis / clathrin-coated endocytic vesicle membrane / Late endosomal microautophagy / ABC-family proteins mediated transport / transmembrane transport / recycling endosome / Aggrephagy / Chaperone Mediated Autophagy / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pze.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pze.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 2pze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/2pze ftp://data.pdbj.org/pub/pdb/validation_reports/pz/2pze | HTTPS FTP |
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-Related structure data
Related structure data | 2pzfC 2pzgC 1xmiS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25525.408 Da / Num. of mol.: 2 / Fragment: CFTR NBD1 387-646(del405-436) / Mutation: del405-436 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR, ABCC7 / Plasmid: modified pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+RIL / References: UniProt: P13569 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.11 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion / pH: 7.5 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 Hepes pH 7.5, 25% PEG 6K; Cryo: 25% DMSO, vapor diffusion, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2006 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→22.094 Å / Num. all: 47121 / Num. obs: 47121 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 5.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XMI Resolution: 1.7→21.296 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: 23.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→21.296 Å
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Refine LS restraints |
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