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- PDB-5uar: Dephosphorylated, ATP-free cystic fibrosis transmembrane conducta... -

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Basic information

Entry
Database: PDB / ID: 5uar
TitleDephosphorylated, ATP-free cystic fibrosis transmembrane conductance regulator (CFTR) from zebrafish
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsMEMBRANE PROTEIN / HYDROLASE / ABC transporter / anion channel / cystic fibrosis
Function / homology
Function and homology information


Kupffer's vesicle development / RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / 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 ...Kupffer's vesicle development / RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / 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 / multicellular organismal-level water homeostasis / germ cell migration / bicarbonate transport / bicarbonate transmembrane transporter activity / pancreas development / embryonic hemopoiesis / chloride channel activity / T cell differentiation / ATPase-coupled transmembrane transporter activity / chloride channel complex / ABC-type transporter activity / cellular response to forskolin / chloride transmembrane transport / recycling endosome membrane / heart development / early endosome membrane / 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
CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. ...CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DECANE / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsZhang, Z. / Chen, J.
CitationJournal: 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
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
SupersessionMar 1, 2017ID: 5TSI
Revision 1.1Mar 1, 2017Group: Other
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,9063
Polymers169,6221
Non-polymers2852
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cystic fibrosis transmembrane conductance regulator / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP- ...ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP-dependent chloride channel


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
#2: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cystic fibrosis transmembrane conductance regulator (CFTR)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 168 kDa/nm / Experimental value: NO
Source (natural)Organism: Danio rerio (zebrafish)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: BacMam
Buffer solutionpH: 7.5
SpecimenConc.: 5.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated defocus min: 800 nm / Calibrated defocus max: 2500 nm / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage 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 opticsEnergyfilter lower: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 3-30

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Processing

EM software
IDNameVersionCategory
1RELION1.4particle selection
2SerialEMimage acquisition
4CTFFIND44.0.17CTF correction
7UCSF Chimeramodel fitting
9RELION1.4initial Euler assignment
10FREALIGNfinal Euler assignment
12FREALIGN3D reconstruction
13REFMACmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 803894
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 803894 / Symmetry type: POINT

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