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- EMDB-8782: Phosphorylated, ATP-bound structure of zebrafish cystic fibrosis ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8782
TitlePhosphorylated, ATP-bound structure of zebrafish cystic fibrosis transmembrane conductance regulator (CFTR)Phosphorylation
Map dataMap with B-factor sharpened
Sample
  • Complex: zebrafish cystic fibrosis transmembrane conductance regulator (CFTR)
    • Protein or peptide: Cystic fibrosis transmembrane conductance regulator
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsCFTR / anion channel / ABC transporter / ATP-bound. / HYDROLASE
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
Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle 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, 2017-
Header (metadata) releaseJul 5, 2017-
Map releaseJul 19, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.9
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5w81
  • Surface level: 1.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8782.png

Downloads & links

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Map

FileDownload / File: emd_8782.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap with B-factor sharpened
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 1.9 / Movie #1: 1.9
Minimum - Maximum-5.55007 - 9.716376
Average (Standard dev.)0.007849435 (±0.20946954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-5.5509.7160.008

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Supplemental data

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Additional map: Original map from Frealign without B-factor sharpening

Fileemd_8782_additional.map
AnnotationOriginal map from Frealign without B-factor sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : zebrafish cystic fibrosis transmembrane conductance regulator (CFTR)

EntireName: zebrafish cystic fibrosis transmembrane conductance regulator (CFTR)
Components
  • Complex: zebrafish cystic fibrosis transmembrane conductance regulator (CFTR)
    • Protein or peptide: Cystic fibrosis transmembrane conductance regulator
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: zebrafish cystic fibrosis transmembrane conductance regulator (CFTR)

SupramoleculeName: zebrafish cystic fibrosis transmembrane conductance regulator (CFTR)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 168 kDa/nm

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Macromolecule #1: Cystic fibrosis transmembrane conductance regulator

MacromoleculeName: Cystic fibrosis transmembrane conductance regulator / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ec: 3.6.3.49
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 169.620812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQRSPVEDAN CLSRYFFWWT NPIMRKGFKE KLRPSDVYQA PSQDAADILA ERLEKEWDRE VASGKKKPSL LRAMARCYIK PFLLFGFLL YIGEATKTVQ PQLLGRIIAS FDPAHEPERA NGYFLAFGLG LLFTARFLLL QPAMFGLHHL GMQIRIALFS I IYKKTLKL ...String:
MQRSPVEDAN CLSRYFFWWT NPIMRKGFKE KLRPSDVYQA PSQDAADILA ERLEKEWDRE VASGKKKPSL LRAMARCYIK PFLLFGFLL YIGEATKTVQ PQLLGRIIAS FDPAHEPERA NGYFLAFGLG LLFTARFLLL QPAMFGLHHL GMQIRIALFS I IYKKTLKL SSRVLDKIST GQLVSLMSAN LGKFDQSLGM AHFIWISPLQ CILCTGLIWE LIDVNSFCAL AAISLLGVLQ AF LSHKMGP YKAQKVLLTN KRLALTSEIM ENLHSVKAYG WEEIMETLIK NIRQDEVKLT RKIGSLRYFY SSAYFFSAIF VIV AAVVPH ALSRGINLRR IFTTLSYCMV LRMTVTRQLP GSIQMWYDTM RLIWKIEEFL SKEEYKLMEY DLSITELELQ DVTA SWDEG PGELLERIKQ ENKANGHHNG DAGLFFTNLY VAPVLKDISL KLKKGEMLAV TGSMGSGKSS LLMTILGELV PSSGK IRHS GRISYSSQTA WIMPGTIRDN ILFGLTYDEY RYKSVVKACQ LEEDLAALPE KDKTPMAEGG LNLSGGQKAR VALARA VYR DADLYLLDAP FTHLDIATEK EIFDKCLCKL MASKTRILVT NKIEHLKRAD KILLLHNGES FFYGTFPELQ SERPDFS SL LLGLEAYDNI SAERRCSILT ETLHRVSVDE SAGMQPERSA FRQVPPTKPM YIDERKASVI VNPLGVARKA SFIQVPEE E VRRTLPDRKF SLVPENELVD ESFMGSDVYH NHGVHMAGQR RQSVLAFMTN AQGQGRREHL QSSFRRRLSV VPQSELASE LDIYTRRLSD STYDMTGILE EENIEACLTD EIDEIEETFE TTKWNTYVRY VSNNKSLLYV LIFILFIAAI EIAGSVAGIF LITDELWRE EHQRSEPNMT KHSNASSSGQ TYAITVTPTS SYYILYIYVA TSESLLAMGF FRGLPFVHTT ITISKKLHQK M LHAVLSAP MSVLNTMKTG RIMNRFTKDM ATIDDMLPLL MFDFVQLTVV VVGCILVVSI VRPYIFLAAT PLAIIFIVMR KY FLRTGQQ LKQLETEARS PIFSHLIMSL KGLWTIRAFE RQAYFEALFH KTLNTHTATW FLYLSTLRWF LFRADILFVF FFT LAAWIA VGTNQDKPGE IGIIICLAML ILGTFQWCVA TSIAVDGMMR SVDRVFKFID LPSETPKPDK GKDSDLIIEN VDAQ ADSSW PHRGQIEVRN LTVKYTEAGH AVLKNLSFSA EGRQRVGILG RTGSGKSSLF NALLKLVYTD GEISIDGVNW NKMPL QKWR KAFGVVPQKV FIFTGPLRMN LDPYGCHSDE ELWRVAEEVG LKTVIEQFPD KLDFQLEYGG YVLSNGHKQL ICLARS ILS GARILLLDQP SAHLDPVTIK VLKKTLRQSF STCTILLSEH KVEPLLECQS FLMMDKGQVK TYDSIQKLLN ETSHLKQ AI SPAERLKLFP RRNSSMRTPQ SKLSSVTQTL QEEAEDNIQD TRLSNSLEVL FQ

UniProtKB: Cystic fibrosis transmembrane conductance regulator

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 61199
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 2 / Number real images: 7434 / Average exposure time: 0.14 sec. / Average electron dose: 1.68 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 900000
Startup modelType of model: EMDB MAP
EMDB ID:

8461

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN (ver. 9.11)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 777102

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