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- EMDB-47982: Chicken BEST1 bound to GABA in an open state -

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Basic information

Entry
Database: EMDB / ID: EMD-47982
TitleChicken BEST1 bound to GABA in an open state
Map data
Sample
  • Complex: Chicken BEST1 bound to GABA in an open state
    • Protein or peptide: Bestrophin 1
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: water
Keywordsbestrophin / ion channel / GABA / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane microdomain / bicarbonate channel activity / transepithelial chloride transport / gamma-aminobutyric acid secretion, neurotransmission / detection of light stimulus involved in visual perception / intracellularly calcium-gated chloride channel activity / glutamate secretion / protein complex oligomerization / regulation of calcium ion transport / chloride channel complex ...membrane microdomain / bicarbonate channel activity / transepithelial chloride transport / gamma-aminobutyric acid secretion, neurotransmission / detection of light stimulus involved in visual perception / intracellularly calcium-gated chloride channel activity / glutamate secretion / protein complex oligomerization / regulation of calcium ion transport / chloride channel complex / regulation of synaptic plasticity / presynapse / basolateral plasma membrane / identical protein binding
Similarity search - Function
Bestrophin / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.95 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 20, 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_47982.png

Downloads & links

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Map

FileDownload / File: emd_47982.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: 0.64
Minimum - Maximum-1.7680428 - 5.2734456
Average (Standard dev.)0.0012243397 (±0.06452896)
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_47982_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47982_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 : Chicken BEST1 bound to GABA in an open state

EntireName: Chicken BEST1 bound to GABA in an open state
Components
  • Complex: Chicken BEST1 bound to GABA in an open state
    • Protein or peptide: Bestrophin 1
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: water

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Supramolecule #1: Chicken BEST1 bound to GABA in an open state

SupramoleculeName: Chicken BEST1 bound to GABA in an open state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 203.5 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: 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

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: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 4 / Number of copies: 5 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 382 / 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: 7.5
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: 43.7 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: 0.6 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: PDB ENTRY
PDB model - PDB ID:

6n28

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 987499
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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