[English] 日本語
Yorodumi- EMDB-8461: Structure of the cystic fibrosis transmembrane conductance regula... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8461 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the cystic fibrosis transmembrane conductance regulator (CFTR) from zebrafish | |||||||||
Map data | Cystic fibrosis transmembrane conductance regulator from zebrafish | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / Kupffer's vesicle development / lymphoid lineage cell migration into thymus / Spemann organizer formation at the embryonic shield / ABC-family proteins mediated transport / regulation of neutrophil chemotaxis / Aggrephagy / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity ...RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / Kupffer's vesicle development / lymphoid lineage cell migration into thymus / Spemann organizer formation at the embryonic shield / ABC-family proteins mediated transport / regulation of neutrophil chemotaxis / 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 transport / bicarbonate transmembrane transporter activity / pancreas development / embryonic hemopoiesis / chloride channel activity / chloride channel complex / T cell differentiation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / chloride transmembrane transport / cellular response to forskolin / isomerase activity / 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 | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.73 Å | |||||||||
Authors | Zhang Z / Chen J | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8461.map.gz | 115.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8461-v30.xml emd-8461.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
Images | emd_8461.png | 212.8 KB | ||
Others | emd_8461_additional.map.gz | 16.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8461 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8461 | HTTPS FTP |
-Validation report
Summary document | emd_8461_validation.pdf.gz | 422.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_8461_full_validation.pdf.gz | 422.3 KB | Display | |
Data in XML | emd_8461_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_8461_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8461 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8461 | HTTPS FTP |
-Related structure data
Related structure data | 5uarMC 8516C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_8461.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cystic fibrosis transmembrane conductance regulator from zebrafish | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: The original map from FREALIGN without b-factor sharpening.
File | emd_8461_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The original map from FREALIGN without b-factor sharpening. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Cystic fibrosis transmembrane conductance regulator or ABCC7
Entire | Name: Cystic fibrosis transmembrane conductance regulator or ABCC7 |
---|---|
Components |
|
-Supramolecule #1: Cystic fibrosis transmembrane conductance regulator or ABCC7
Supramolecule | Name: Cystic fibrosis transmembrane conductance regulator or ABCC7 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Danio rerio (zebrafish) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK 293S GnTI- / Recombinant plasmid: pEG Bacmam |
Molecular weight | Experimental: 168 kDa/nm |
-Macromolecule #1: Cystic fibrosis transmembrane conductance regulator
Macromolecule | Name: 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 weight | Theoretical: 169.605734 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: DECANE
Macromolecule | Name: DECANE / type: ligand / ID: 2 / Number of copies: 2 / Formula: D10 |
---|---|
Molecular weight | Theoretical: 142.282 Da |
Chemical component information | ChemComp-D10: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59524 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |