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- PDB-6d3r: Thermostablilized dephosphorylated chicken CFTR -

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Basic information

Entry
Database: PDB / ID: 6d3r
TitleThermostablilized dephosphorylated chicken CFTR
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsMEMBRANE PROTEIN / CFTR
Function / homology
Function and homology information


RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / ABC-family proteins mediated transport / Cargo recognition for clathrin-mediated endocytosis / Aggrephagy / Clathrin-mediated endocytosis / Ub-specific processing proteases / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / bicarbonate transport ...RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / ABC-family proteins mediated transport / Cargo recognition for clathrin-mediated endocytosis / Aggrephagy / Clathrin-mediated endocytosis / Ub-specific processing proteases / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / bicarbonate transport / chloride channel complex / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / chloride transmembrane transport / isomerase activity / transmembrane transport / recycling endosome membrane / early endosome membrane / apical plasma membrane / endoplasmic reticulum membrane / 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. / ABC transporter ...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
ADENOSINE-5'-TRIPHOSPHATE / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsFay, J.F. / Riordan, J.R.
CitationJournal: Biochemistry / Year: 2018
Title: Cryo-EM Visualization of an Active High Open Probability CFTR Anion Channel.
Authors: Jonathan F Fay / Luba A Aleksandrov / Timothy J Jensen / Liying L Cui / Joseph N Kousouros / Lihua He / Andrei A Aleksandrov / Drew S Gingerich / John R Riordan / James Z Chen /
Abstract: The cystic fibrosis transmembrane conductance regulator (CFTR) anion channel, crucial to epithelial salt and water homeostasis, and defective due to mutations in its gene in patients with cystic ...The cystic fibrosis transmembrane conductance regulator (CFTR) anion channel, crucial to epithelial salt and water homeostasis, and defective due to mutations in its gene in patients with cystic fibrosis, is a unique member of the large family of ATP-binding cassette transport proteins. Regulation of CFTR channel activity is stringently controlled by phosphorylation and nucleotide binding. Structural changes that underlie transitions between active and inactive functional states are not yet fully understood. Indeed the first 3D structures of dephosphorylated, ATP-free, and phosphorylated ATP-bound states were only recently reported. Here we have determined the structure of inactive and active states of a thermally stabilized CFTR, the latter with a very high channel open probability, confirmed after reconstitution into proteoliposomes. These structures, obtained at nominal resolution of 4.3 and 6.6 Å, reveal a unique repositioning of the transmembrane helices and regulatory domain density that provide insights into the structural transition between active and inactive functional states of CFTR. Moreover, we observe an extracellular vestibule that may provide anion access to the pore due to the conformation of transmembrane helices 7 and 8 that differs from the previous orthologue CFTR structures. In conclusion, our work contributes detailed structural information on an active, open state of the CFTR anion channel.
History
DepositionApr 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 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)163,6523
Polymers162,6371
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1170 Å2
ΔGint-7 kcal/mol
Surface area57080 Å2

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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: 162637.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CFTR / Cell line (production host): BHK / Production host: Cricetinae (hamsters) / References: UniProt: A0A1D5PBN0*PLUS, EC: 3.6.3.49
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: CFTR / Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Gallus gallus (chicken)
Source (recombinant)Organism: Cricetinae (hamsters) / Cell: BHK / Plasmid: pNUT
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4RELIONCTF correction
7Rosettamodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13Rosettamodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Num. of particles: 30219 / Symmetry type: POINT

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