MEMBRANE PROTEIN / ion channel / calcium activated chloride channel / eukaryotic membrane protein / anion channel / transport protein / ligand gated ion channel
Function / homology
Bestrophin / Bestrophin/UPF0187 / Bestrophin-1 / Bestrophin, RFP-TM, chloride channel / Stimuli-sensing channels / transepithelial chloride transport / detection of light stimulus involved in visual perception / chloride channel activity / chloride channel complex / regulation of calcium ion transport ...Bestrophin / Bestrophin/UPF0187 / Bestrophin-1 / Bestrophin, RFP-TM, chloride channel / Stimuli-sensing channels / transepithelial chloride transport / detection of light stimulus involved in visual perception / chloride channel activity / chloride channel complex / regulation of calcium ion transport / basolateral plasma membrane / identical protein binding / metal ion binding / Bestrophin homolog
Function and homology information
Specimen source
Gallus gallus (chicken)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.9 Å resolution
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.
Average exposure time: 10 sec. / Electron dose: 76 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1
Image scans
Movie frames/image: 40 / Used frames/image: 1-40
-
Processing
EM software
ID
Name
Version
Category
1
RELION
2.1
particleselection
4
RELION
2.1
CTFcorrection
7
Coot
0.8.9.1
modelfitting
9
PHENIX
1.13
modelrefinement
10
RELION
2.1
initialEulerassignment
11
RELION
2.1
finalEulerassignment
12
RELION
2.1
classification
13
RELION
2.1
3Dreconstruction
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
Point symmetry: C5
3D reconstruction
Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 41484 / Algorithm: FOURIER SPACE / Number of class averages: 2 / Symmetry type: POINT
Atomic model building
Overall b value: 55.9 / Ref protocol: OTHER / Ref space: REAL
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi