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- EMDB-47997: Human BEST1 in an open state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47997
TitleHuman BEST1 in an open state
Map data
Sample
  • Complex: Human BEST1 in an open state
    • Protein or peptide: Bestrophin-1
  • Ligand: CALCIUM ION
  • Ligand: water
Keywordsbestrophin / ion channel / GABA / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane microdomain / bicarbonate channel activity / gamma-aminobutyric acid secretion, neurotransmission / transepithelial chloride transport / ligand-gated channel activity / intracellularly calcium-gated chloride channel activity / detection of light stimulus involved in visual perception / bicarbonate transmembrane transporter activity / glutamate secretion / chloride transport ...membrane microdomain / bicarbonate channel activity / gamma-aminobutyric acid secretion, neurotransmission / transepithelial chloride transport / ligand-gated channel activity / intracellularly calcium-gated chloride channel activity / detection of light stimulus involved in visual perception / bicarbonate transmembrane transporter activity / glutamate secretion / chloride transport / chloride channel activity / protein complex oligomerization / regulation of calcium ion transport / chloride channel complex / visual perception / basal plasma membrane / regulation of synaptic plasticity / Stimuli-sensing channels / presynapse / monoatomic ion transmembrane transport / basolateral plasma membrane / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Bestrophin / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsPant S / Long SB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: The pentameric chloride channel BEST1 is activated by extracellular GABA.
Authors: Swati Pant / Stephanie W Tam / Stephen B Long /
Abstract: Bestrophin-1 (BEST1) is a chloride channel expressed in the eye and other tissues of the body. A link between BEST1 and the principal inhibitory neurotransmitter -aminobutyric acid (GABA) has been ...Bestrophin-1 (BEST1) is a chloride channel expressed in the eye and other tissues of the body. A link between BEST1 and the principal inhibitory neurotransmitter -aminobutyric acid (GABA) has been proposed. The most appreciated receptors for extracellular GABA are the GABA G-protein-coupled receptors and the pentameric GABA chloride channels, both of which have fundamental roles in the central nervous system. Here, we demonstrate that BEST1 is directly activated by GABA. Through functional studies and atomic-resolution structures of human and chicken BEST1, we identify a GABA binding site on the channel's extracellular side and determine the mechanism by which GABA binding stabilizes opening of the channel's central gate. This same gate, "the neck," is activated by intracellular [Ca], indicating that BEST1 is controlled by ligands from both sides of the membrane. The studies demonstrate that BEST1, which shares no structural homology with GABA receptors, is a GABA-activated chloride channel. The physiological implications of this finding remain to be studied.
History
DepositionNov 21, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47997.png

Downloads & links

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Map

FileDownload / File: emd_47997.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.77
Minimum - Maximum-3.2849402 - 4.946384
Average (Standard dev.)0.00049599627 (±0.07401806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47997_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47997_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human BEST1 in an open state

EntireName: Human BEST1 in an open state
Components
  • Complex: Human BEST1 in an open state
    • Protein or peptide: Bestrophin-1
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Human BEST1 in an open state

SupramoleculeName: Human BEST1 in an open state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 237 kDa/nm

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Macromolecule #1: Bestrophin-1

MacromoleculeName: Bestrophin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.416449 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: TITYTSQVAN ARLGSFSRLL LCWRGSIYKL LYGEFLIFLL CYYIIRFIYR LALTEEQQLM FEKLTLYCDS YIQLIPISFV LGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA G FMTPAEHK ...String:
TITYTSQVAN ARLGSFSRLL LCWRGSIYKL LYGEFLIFLL CYYIIRFIYR LALTEEQQLM FEKLTLYCDS YIQLIPISFV LGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA G FMTPAEHK QLEKLSLPHN MFWVPWVWFA NLSMKAWLGG RIRDPILLQS LLNEMNTLRT QCGHLYAYDW ISIPLVYTQV VT VAVYSFF LTCLVGRQFL NPAKAYPGHE LDLVVPVFTF LQFFFYVGWL KVAEQLINPF GEDDDDFETN WIVDRNLQVS LLA VDEMHQ DLPRMEPDMY WNKPEPQPPY TAASAQFRRA SFMGSTFNIS LNKEEMEFQP NQEDEEDAHA GIIGRFLGLQ SSNS LEVLF Q

UniProtKB: Bestrophin-1

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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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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 269 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107143
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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