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Yorodumi- PDB-5uar: Dephosphorylated, ATP-free cystic fibrosis transmembrane conducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uar | |||||||||
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Title | Dephosphorylated, ATP-free cystic fibrosis transmembrane conductance regulator (CFTR) from zebrafish | |||||||||
Components | Cystic fibrosis transmembrane conductance regulator | |||||||||
Keywords | MEMBRANE PROTEIN / HYDROLASE / ABC transporter / anion channel / cystic fibrosis | |||||||||
Function / homology | Function and homology information RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / Kupffer's vesicle development / lymphoid lineage cell migration into thymus / Spemann organizer formation at the embryonic shield / ABC-family proteins mediated transport / regulation of neutrophil chemotaxis / Aggrephagy / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity ...RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / Kupffer's vesicle development / lymphoid lineage cell migration into thymus / Spemann organizer formation at the embryonic shield / ABC-family proteins mediated transport / regulation of neutrophil chemotaxis / Aggrephagy / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / transepithelial water transport / respiratory burst involved in defense response / germ cell migration / multicellular organismal-level water homeostasis / bicarbonate transport / bicarbonate transmembrane transporter activity / pancreas development / embryonic hemopoiesis / chloride channel activity / chloride channel complex / T cell differentiation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / cellular response to forskolin / chloride transmembrane transport / isomerase activity / recycling endosome membrane / early endosome membrane / heart development / defense response to bacterium / apical plasma membrane / innate immune response / endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å | |||||||||
Authors | Zhang, Z. / Chen, J. | |||||||||
Citation | Journal: Cell / Year: 2016 Title: Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator. Authors: Zhe Zhang / Jue Chen / Abstract: The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of ...The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues. A single gate near the extracellular surface closes the channel. The regulatory domain, dephosphorylated, is located in the intracellular opening between the two nucleotide-binding domains (NBDs), preventing NBD dimerization and channel opening. The structure also reveals why many cystic-fibrosis-causing mutations would lead to defects either in folding, ion conduction, or gating and suggests new avenues for therapeutic intervention. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5uar.cif.gz | 252 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uar.ent.gz | 196.5 KB | Display | PDB format |
PDBx/mmJSON format | 5uar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uar_validation.pdf.gz | 779.2 KB | Display | wwPDB validaton report |
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Full document | 5uar_full_validation.pdf.gz | 779 KB | Display | |
Data in XML | 5uar_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 5uar_validation.cif.gz | 51.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/5uar ftp://data.pdbj.org/pub/pdb/validation_reports/ua/5uar | HTTPS FTP |
-Related structure data
Related structure data | 8461MC 8516C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 169621.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cftr / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q1LX78, EC: 3.6.3.49 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cystic fibrosis transmembrane conductance regulator (CFTR) Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 168 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Danio rerio (zebrafish) |
Source (recombinant) | Organism: Homo sapiens (human) / Plasmid: BacMam |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated defocus min: 800 nm / Calibrated defocus max: 2500 nm / Cs: 0.01 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 7 sec. / Electron dose: 1.54 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5768 |
EM imaging optics | Energyfilter lower: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 3-30 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 803894 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 803894 / Symmetry type: POINT |