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- EMDB-9326: BEST1 calcium-bound open state -

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Basic information

Entry
Database: EMDB / ID: EMD-9326
TitleBEST1 calcium-bound open state
Map dataBEST1 calcium-bound open state
Sample
  • Complex: BEST1 calcium-bound open state
    • Protein or peptide: Bestrophin homolog
  • Ligand: CALCIUM IONCalcium
Function / homologyBestrophin-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 speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMiller AN / Vaisey G / Long SB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110396 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA008748 United States
CitationJournal: 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
DepositionNov 12, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJan 23, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0503
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0503
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n28
  • Surface level: 0.0503
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_9326.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBEST1 calcium-bound open state
Voxel sizeX=Y=Z: 1.088 Å
Density
Contour LevelBy AUTHOR: 0.0503 / Movie #1: 0.0503
Minimum - Maximum-0.06675466 - 0.15745859
Average (Standard dev.)0.0007282378 (±0.010355358)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 163.20001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0881.0881.088
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z163.200163.200163.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0670.1570.001

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Supplemental data

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Sample components

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Entire : BEST1 calcium-bound open state

EntireName: BEST1 calcium-bound open state
Components
  • Complex: BEST1 calcium-bound open state
    • Protein or peptide: Bestrophin homolog
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: BEST1 calcium-bound open state

SupramoleculeName: BEST1 calcium-bound open state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)
Recombinant expressionOrganism: Komagataella pastoris (fungus)

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Macromolecule #1: Bestrophin homolog

MacromoleculeName: Bestrophin homolog / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 40.761727 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: 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

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 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 mg/mL
BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 2.1)
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 41484

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Chain ID: A / Chain - Residue range: 2-367
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 55.9
Output model

PDB-6n28:
BEST1 calcium-bound open state

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