+Open data
-Basic information
Entry | Database: PDB / ID: 6gju | ||||||
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Title | human NBD1 of CFTR in complex with nanobodies T2a and T4 | ||||||
Components |
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Keywords | HYDROLASE / Cystic Fibrosis / CFTR / nanobodies / thermal stabilization / conformational dynamics | ||||||
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 / establishment of localization in cell / PDZ domain binding / 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) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Sigoillot, M. / Overtus, M. / Grodecka, M. / Scholl, D. / Garcia-Pino, A. / Laeremans, T. / He, L. / Pardon, E. / Hildebrandt, E. / Urbatsch, I. ...Sigoillot, M. / Overtus, M. / Grodecka, M. / Scholl, D. / Garcia-Pino, A. / Laeremans, T. / He, L. / Pardon, E. / Hildebrandt, E. / Urbatsch, I. / Steyaert, J. / Riordan, J.R. / Govaerts, C. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Domain-interface dynamics of CFTR revealed by stabilizing nanobodies. Authors: Sigoillot, M. / Overtus, M. / Grodecka, M. / Scholl, D. / Garcia-Pino, A. / Laeremans, T. / He, L. / Pardon, E. / Hildebrandt, E. / Urbatsch, I. / Steyaert, J. / Riordan, J.R. / Govaerts, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gju.cif.gz | 177.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gju.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/6gju ftp://data.pdbj.org/pub/pdb/validation_reports/gj/6gju | HTTPS FTP |
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-Related structure data
Related structure data | 6gjqC 6gjsC 6gk4C 6gkdC 1melS 2pzeS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29218.408 Da / Num. of mol.: 1 / Mutation: S492P,A534P,I539T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR / Production host: Escherichia coli (E. coli) References: UniProt: Q20BJ8, UniProt: P13569*PLUS, EC: 3.6.3.49 |
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-Antibody , 2 types, 2 molecules BC
#2: Antibody | Mass: 15488.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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#3: Antibody | Mass: 15820.306 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 3 types, 85 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-PEG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium sulfate, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.4 Å / Num. obs: 17227 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 101.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1204 / Rrim(I) all: 0.1311 / Net I/σ(I): 15.39 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.1204 / Num. unique obs: 16001 / CC1/2: 0.997 / Rrim(I) all: 0.1311 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PZE and 1MEL Resolution: 2.6→46.4 Å / Cor.coef. Fo:Fc: 0.9057 / Cor.coef. Fo:Fc free: 0.8988 / SU R Cruickshank DPI: 0.602 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.659 / SU Rfree Blow DPI: 0.285 / SU Rfree Cruickshank DPI: 0.285
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Displacement parameters | Biso mean: 77.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.452 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.78 Å / Total num. of bins used: 8
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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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