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- PDB-5w81: Phosphorylated, ATP-bound structure of zebrafish cystic fibrosis ... -

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Basic information

Entry
Database: PDB / ID: 5w81
TitlePhosphorylated, ATP-bound structure of zebrafish cystic fibrosis transmembrane conductance regulator (CFTR)
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsHYDROLASE / CFTR / anion channel / ABC transporter / ATP-bound.
Function / homology
Function and homology information


ABC-family proteins mediated transport / RHO GTPases regulate CFTR trafficking / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / RHOQ GTPase cycle / Kupffer's vesicle development / lymphoid lineage cell migration into thymus / Spemann organizer formation at the embryonic shield / regulation of neutrophil chemotaxis / Ub-specific processing proteases ...ABC-family proteins mediated transport / RHO GTPases regulate CFTR trafficking / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / RHOQ GTPase cycle / Kupffer's vesicle development / lymphoid lineage cell migration into thymus / Spemann organizer formation at the embryonic shield / regulation of neutrophil chemotaxis / Ub-specific processing proteases / Aggrephagy / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / transepithelial water transport / germ cell migration / respiratory burst involved in defense response / multicellular organismal-level water homeostasis / bicarbonate transmembrane transporter activity / bicarbonate transport / 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 / isomerase activity / 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. / 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 speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsZhang, Z. / Liu, F. / Chen, J.
CitationJournal: Cell / Year: 2017
Title: Conformational Changes of CFTR upon Phosphorylation and ATP Binding.
Authors: Zhe Zhang / Fangyu Liu / Jue Chen /
Abstract: The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from an ATP-binding cassette transporter. CFTR channel gating is strictly coupled to phosphorylation and ATP ...The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from an ATP-binding cassette transporter. CFTR channel gating is strictly coupled to phosphorylation and ATP hydrolysis. Previously, we reported essentially identical structures of zebrafish and human CFTR in the dephosphorylated, ATP-free form. Here, we present the structure of zebrafish CFTR in the phosphorylated, ATP-bound conformation, determined by cryoelectron microscopy to 3.4 Å resolution. Comparison of the two conformations shows major structural rearrangements leading to channel opening. The phosphorylated regulatory domain is disengaged from its inhibitory position; the nucleotide-binding domains (NBDs) form a "head-to-tail" dimer upon binding ATP; and the cytoplasmic pathway, found closed off in other ATP-binding cassette transporters, is cracked open, consistent with CFTR's unique channel function. Unexpectedly, the extracellular mouth of the ion pore remains closed, indicating that local movements of the transmembrane helices can control ion access to the pore even in the NBD-dimerized conformation.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.3Mar 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)170,6845
Polymers169,6211
Non-polymers1,0634
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
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: 169620.812 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- / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: Q1LX78, EC: 3.6.3.49
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: zebrafish 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) / Cell: HEK293S GnTI-
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
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 FIELDBright-field microscopy / Nominal magnification: 61199 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 0.14 sec. / Electron dose: 1.68 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 7434
Image scansWidth: 7420 / Height: 7676 / Movie frames/image: 50 / Used frames/image: 1-50

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Processing

EM software
IDNameVersionCategory
1RELION1.4particle selection
2SerialEMimage acquisition
4CTFFIND4.0.17CTF correction
7PHENIXmodel fitting
9REFMACmodel refinement
10RELION2initial Euler assignment
11FREALIGN9.11final Euler assignment
12RELION2classification
13FREALIGN9.113D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 900000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 777102 / Symmetry type: POINT

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