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- EMDB-8461: Structure of the cystic fibrosis transmembrane conductance regula... -

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Basic information

Entry
Database: EMDB / ID: EMD-8461
TitleStructure of the cystic fibrosis transmembrane conductance regulator (CFTR) from zebrafish
Map dataCystic fibrosis transmembrane conductance regulator from zebrafish
Sample
  • Complex: Cystic fibrosis transmembrane conductance regulator or ABCC7
    • Protein or peptide: Cystic fibrosis transmembrane conductance regulator
  • Ligand: DECANE
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: 3.73 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
DepositionOct 28, 2016-
Header (metadata) releaseNov 30, 2016-
Map releaseDec 7, 2016-
UpdateSep 12, 2018-
Current statusSep 12, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5uar
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8461.png

Downloads & links

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Map

FileDownload / File: emd_8461.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCystic fibrosis transmembrane conductance regulator from zebrafish
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.429 / Movie #1: 1.5
Minimum - Maximum-3.7585912 - 6.1549664
Average (Standard dev.)0.012612341 (±0.19569404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-69-50-137
NX/NY/NZ136114193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-3.7596.1550.013

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Supplemental data

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Additional map: The original map from FREALIGN without b-factor sharpening.

Fileemd_8461_additional.map
AnnotationThe original 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 : Cystic fibrosis transmembrane conductance regulator or ABCC7

EntireName: Cystic fibrosis transmembrane conductance regulator or ABCC7
Components
  • Complex: Cystic fibrosis transmembrane conductance regulator or ABCC7
    • Protein or peptide: Cystic fibrosis transmembrane conductance regulator
  • Ligand: DECANE

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Supramolecule #1: Cystic fibrosis transmembrane conductance regulator or ABCC7

SupramoleculeName: Cystic fibrosis transmembrane conductance regulator or ABCC7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293S GnTI- / Recombinant plasmid: pEG Bacmam
Molecular weightExperimental: 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: 169.605734 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 SAERRSSILT 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 GARILLLDEP SAHLDPVTIK VLKKTLRQSF STCTILLSEH KVEPLLECQS FLMMDKGQVK TYDSIQKLLN ETSHLKQ AI SPAERLKLFP RRNSSMRTPQ SKLSSVTQTL QEEAEDNIQD TRLSNSLEVL FQ

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Macromolecule #2: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 2 / Number of copies: 2 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE / Decane

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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 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK I

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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 / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59524
Specialist opticsEnergy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 3-30 / Number grids imaged: 1 / Number real images: 5700 / Average exposure time: 0.14 sec. / Average electron dose: 1.54 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 840000
CTF correctionSoftware - Name: CTFFIND4 (ver. 4.0.17)
Startup modelType of model: EMDB MAP
EMDB ID:

6533

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 803894

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