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- EMDB-8516: Structure of human cystic fibrosis transmembrane conductance regu... -

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Basic information

Entry
Database: EMDB / ID: 8516
TitleStructure of human cystic fibrosis transmembrane conductance regulator (CFTR)
Map dataHuman cystic fibrosis transmembrane conductance regulator without B factor sharpening (FREALIGN)
SampleCystic fibrosis transmembrane conductance regulator or ABCC7
  • (Cystic fibrosis transmembrane conductance ...) x 2
Function / homologyCystic fibrosis TM conductance regulator (CFTR), regulator domain / ABC transporter-like / ABC transporter type 1, transmembrane domain / ABC transporter, conserved site / CFTR regulator domain / P-loop containing nucleoside triphosphate hydrolase / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter transmembrane region / ABC transporters family signature. ...Cystic fibrosis TM conductance regulator (CFTR), regulator domain / ABC transporter-like / ABC transporter type 1, transmembrane domain / ABC transporter, conserved site / CFTR regulator domain / P-loop containing nucleoside triphosphate hydrolase / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter transmembrane region / ABC transporters family signature. / AAA+ ATPase domain / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporter integral membrane type-1 fused domain profile. / ABC-family proteins mediated transport / RHO GTPases regulate CFTR trafficking / Defective CFTR causes cystic fibrosis / Ub-specific processing proteases / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / Cystic fibrosis transmembrane conductance regulator / ATPase-coupled anion transmembrane transporter activity / positive regulation of cyclic nucleotide-gated ion channel activity / positive regulation of voltage-gated chloride channel activity / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / transepithelial water transport / intracellular pH elevation / bicarbonate transmembrane transporter activity / Golgi-associated vesicle membrane / multicellular organismal water homeostasis / chloride transmembrane transporter activity / chloride channel regulator activity / chloride channel inhibitor activity / chloride channel activity / vesicle docking involved in exocytosis / chloride channel complex / chloride transmembrane transport / cholesterol transport / membrane hyperpolarization / positive regulation of exocytosis / cellular response to forskolin / ATPase activity, coupled to transmembrane movement of substances / positive regulation of insulin secretion involved in cellular response to glucose stimulus / sperm capacitation / cholesterol biosynthetic process / recycling endosome / clathrin-coated vesicle membrane / PDZ domain binding / cellular response to cAMP / recycling endosome membrane / transmembrane transport / lysosomal membrane / bicarbonate transport / membrane organization / early endosome membrane / apical plasma membrane / ATPase activity / early endosome / endosome membrane / protein deubiquitination / endoplasmic reticulum membrane / integral component of plasma membrane / cell surface / enzyme binding / protein-containing complex / integral component of membrane / extracellular exosome / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm / Cystic fibrosis transmembrane conductance regulator
Function and homology information
SourceHomo sapiens / / human
Methodsingle particle reconstruction / cryo EM / 3.87 Å resolution
AuthorsLiu F / Zhang Z / Chen J
CitationJournal: Cell / Year: 2017
Title: Molecular Structure of the Human CFTR Ion Channel.
Authors: Fangyu Liu / Zhe Zhang / László Csanády / David C Gadsby / Jue Chen
Abstract: The cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-binding cassette (ABC) transporter that uniquely functions as an ion channel. Here, we present a 3.9 Å structure of ...The cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-binding cassette (ABC) transporter that uniquely functions as an ion channel. Here, we present a 3.9 Å structure of dephosphorylated human CFTR without nucleotides, determined by electron cryomicroscopy (cryo-EM). Close resemblance of this human CFTR structure to zebrafish CFTR under identical conditions reinforces its relevance for understanding CFTR function. The human CFTR structure reveals a previously unresolved helix belonging to the R domain docked inside the intracellular vestibule, precluding channel opening. By analyzing the sigmoid time course of CFTR current activation, we propose that PKA phosphorylation of the R domain is enabled by its infrequent spontaneous disengagement, which also explains residual ATPase and gating activity of dephosphorylated CFTR. From comparison with MRP1, a feature distinguishing CFTR from all other ABC transporters is the helix-loop transition in transmembrane helix 8, which likely forms the structural basis for CFTR's channel function.
Copyright: 2017 Elsevier Inc. All rights reserved.
Validation ReportPDB-ID: 5uak

SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2016 / Header (metadata) release: Dec 21, 2016 / Map release: Dec 21, 2016 / Last update: Jan 18, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5uak
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

Fileemd_8516.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
0.82 Å/pix.
= 313.728 Å
384 pix
0.82 Å/pix.
= 313.728 Å
384 pix
0.82 Å/pix.
= 313.728 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.817 Å
Density
Contour Level:0.511 (by author), 0.9 (movie #1):
Minimum - Maximum-1.2391155 - 3.1540349
Average (Standard dev.)-0.035532568 (0.1034285)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 313.728 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8170.8170.817
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z313.728313.728313.728
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.2393.154-0.036

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Supplemental data

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Sample components

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Entire Cystic fibrosis transmembrane conductance regulator or ABCC7

EntireName: Cystic fibrosis transmembrane conductance regulator or ABCC7
Number of components: 3

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Component #1: protein, Cystic fibrosis transmembrane conductance regulator or ABCC7

ProteinName: Cystic fibrosis transmembrane conductance regulator or ABCC7
Recombinant expression: No
SourceSpecies: Homo sapiens / / human
Source (engineered)Expression System: Homo sapiens / / human / Vector: pEG Bacmam / Cell of expression system: HEK 293S GnTI-

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Component #2: protein, Cystic fibrosis transmembrane conductance regulator

ProteinName: Cystic fibrosis transmembrane conductance regulator / Recombinant expression: No
MassTheoretical: 169.353578 kDa
Source (engineered)Expression System: Homo sapiens / / human

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Component #3: protein, Cystic fibrosis transmembrane conductance regulator

ProteinName: Cystic fibrosis transmembrane conductance regulator / Recombinant expression: No
MassTheoretical: 1.549902 kDa
Source (engineered)Expression System: Homo sapiens / / human

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.68 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 61200 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2500 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3642

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 415915
3D reconstructionSoftware: FREALIGN / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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