+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9324 | |||||||||
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Title | BEST1 calcium-free closed state | |||||||||
Map data | BEST1 calcium-free closed state | |||||||||
Sample |
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Function / homology | Bestrophin-1 / Stimuli-sensing channels / Bestrophin / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / chloride channel activity / membrane / metal ion binding / Bestrophin 1 Function and homology information | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Miller AN / Vaisey G / Long SB | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2019 Title: Molecular mechanisms of gating in the calcium-activated chloride channel bestrophin. Authors: Alexandria N Miller / George Vaisey / Stephen B Long / Abstract: Bestrophin (BEST1-4) ligand-gated chloride (Cl) channels are activated by calcium (Ca). Mutation of BEST1 causes retinal disease. Partly because bestrophin channels have no sequence or structural ...Bestrophin (BEST1-4) ligand-gated chloride (Cl) channels are activated by calcium (Ca). Mutation of BEST1 causes retinal disease. Partly because bestrophin channels have no sequence or structural similarity to other ion channels, the molecular mechanisms underlying gating are unknown. Here, we present a series of cryo-electron microscopy structures of chicken BEST1, determined at 3.1 Å resolution or better, that represent the channel's principal gating states. Unlike other channels, opening of the pore is due to the repositioning of tethered pore-lining helices within a surrounding protein shell that dramatically widens a neck of the pore through a concertina of amino acid rearrangements. The neck serves as both the activation and the inactivation gate. Ca binding instigates opening of the neck through allosteric means whereas inactivation peptide binding induces closing. An aperture within the otherwise wide pore controls anion permeability. The studies define a new molecular paradigm for gating among ligand-gated ion channels. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9324.map.gz | 12 MB | EMDB map data format | |
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Header (meta data) | emd-9324-v30.xml emd-9324.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_9324.png | 187.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9324 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9324 | HTTPS FTP |
-Validation report
Summary document | emd_9324_validation.pdf.gz | 529.8 KB | Display | EMDB validaton report |
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Full document | emd_9324_full_validation.pdf.gz | 529.4 KB | Display | |
Data in XML | emd_9324_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_9324_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9324 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9324 | HTTPS FTP |
-Related structure data
Related structure data | 6n26MC 9321C 9322C 9323C 9325C 9326C 6n23C 6n24C 6n25C 6n27C 6n28C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9324.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | BEST1 calcium-free closed state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.088 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : BEST1 calcium-free closed state
Entire | Name: BEST1 calcium-free closed state |
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Components |
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-Supramolecule #1: BEST1 calcium-free closed state
Supramolecule | Name: BEST1 calcium-free closed state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Gallus gallus (chicken) |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
-Macromolecule #1: Bestrophin homolog
Macromolecule | Name: Bestrophin homolog / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 40.761727 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: TVTYTNRVAD ARLGTFSQLL LQWKGSIYKL LYSEFLIFIS LYFAISLVYR LILSESQRLM FEKLALYCNS YAELIPVSFV LGFYVSLVV SRWWAQYESI PWPDRIMNLV SCNVDGEDEY GRLLRRTLMR YSNLCSVLIL RSVSTAVYKR FPSMEHVVRA G LMTPEEHK ...String: TVTYTNRVAD ARLGTFSQLL LQWKGSIYKL LYSEFLIFIS LYFAISLVYR LILSESQRLM FEKLALYCNS YAELIPVSFV LGFYVSLVV SRWWAQYESI PWPDRIMNLV SCNVDGEDEY GRLLRRTLMR YSNLCSVLIL RSVSTAVYKR FPSMEHVVRA G LMTPEEHK KFESLNSPHN KFWIPCVWFS NLAVKARNEG RIRDSVLLQG ILNELNTLRS QCGRLYGYDW ISIPLVYTQV VT VAVYSFF LACLIGRQFL DPEKAYPGHE LDLFVPVFTF LQFFFYAGWL KVAEQLINPF GEDDDDFETN WLIDRNLQVS LMA VDEMHQ DLPILEKDLY WNEPDPQEGE EF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 76.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |