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- PDB-6uk1: Crystal structure of nucleotide-binding domain 2 (NBD2) of the hu... -
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Basic information
Entry | Database: PDB / ID: 6uk1 | ||||||
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Title | Crystal structure of nucleotide-binding domain 2 (NBD2) of the human Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) | ||||||
![]() | Cystic fibrosis transmembrane conductance regulator | ||||||
![]() | HYDROLASE / NBD2 / CFTR / ABC transport | ||||||
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. / Vorobiev, S.M. / Vernon, R.M. / Khazanov, N. / Senderowitz, H. / Forman-Kay, J.D. / Hunt, J.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A thermodynamically stabilized form of the second nucleotide binding domain from human CFTR shows a catalytically inactive conformation Authors: Wang, C. / Vorobiev, S. / Vernon, R.M. / Khazanov, N. / Senderowitz, H. / Forman-Kay, J.D. / Hunt, J.F. #1: ![]() Title: Mutational stabilization of the second nucleotide binding domain (NBD2) of CFTR yields soluble protein and insight into NBD2 disease-causing mutations Authors: Vernon, R.M. / Chong, P.A. / Lin, H. / Yang, Z. / Zhou, Q. / Aleksandrov, A.A. / An, J. / Protasevich, I. / Dawson, J.E. / Riordan, J.R. / Thibodeau, P.H. / Brouillette, C.G. / Forman-Kay, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 358.1 KB | Display | ![]() |
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PDB format | ![]() | 291.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 35.8 KB | Display | |
Data in CIF | ![]() | 46 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gd7S 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25552.297 Da / Num. of mol.: 4 Mutation: S1255L,Q1280E,K1292D,Y1307N,K1334G,S1359A,Q1411D,H1402A,Q1411D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P13569, channel-conductance-controlling ATPase #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.58 % |
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Crystal grow | Temperature: 277 K / Method: microbatch Details: 24% PEG 8000, 100 mM Li2SO4, 10mM NaBr, 100 mM Bis-Tris Propane pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.693→100 Å / Num. obs: 32360 / % possible obs: 99 % / Redundancy: 5 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.116 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.7→5.98 Å / Num. unique obs: 28962 / Rpim(I) all: 0.05 / Rrim(I) all: 0.116 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GD7 Resolution: 2.693→64.414 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 41.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.42 Å2 / Biso mean: 52.7125 Å2 / Biso min: 5.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.693→64.414 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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