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- EMDB-62247: Cryo-EM structure of docked mouse bestrophin-1 in a closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-62247
TitleCryo-EM structure of docked mouse bestrophin-1 in a closed state
Map data
Sample
  • Complex: Docked Pentameric structure of mouse bestrophin-1 in a closed state
    • Protein or peptide: Bestrophin-1,Soluble cytochrome b562
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION
KeywordsDocked / closed / Calcium-bound / 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 / Stimuli-sensing channels / 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 / Stimuli-sensing channels / glutamate secretion / chloride transport / chloride channel activity / protein complex oligomerization / regulation of calcium ion transport / chloride channel complex / electron transport chain / regulation of synaptic plasticity / presynapse / basolateral plasma membrane / periplasmic space / electron transfer activity / iron ion binding / heme binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Bestrophin / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Bestrophin-1 / Soluble cytochrome b562
Similarity search - Component
Biological speciesMus musculus (house mouse) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLim HH / Kim KW / Ko A
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C1004884 Korea, Republic Of
National Research Foundation (NRF, Korea)2020 M3E5D907 Korea, Republic Of
CitationJournal: Mol Cells / Year: 2025
Title: Cryo-EM structures of mouse bestrophin 1 channel in closed and partially open conformations.
Authors: Kwon-Woo Kim / Euna Lee / Ara Ko / Junmo Hwang / Kunwoong Park / Byoung-Cheol Lee / Ki Woo Kim / Won-Jong Oh / Kyuhyung Kim / Hyun-Ho Lim /
Abstract: Bestrophin 1 (BEST1) channels are calcium-activated Cl channels involved in diverse physiological processes, including gliotransmitter release in astrocytes. Although human and chicken BEST1 ...Bestrophin 1 (BEST1) channels are calcium-activated Cl channels involved in diverse physiological processes, including gliotransmitter release in astrocytes. Although human and chicken BEST1 orthologs have been extensively studied, the structural and functional properties of mouse BEST1 (mBEST1) remain poorly understood. In this study, we characterized the structure-function of mBEST1-BF, a C-terminally tagged variant, using whole-cell patch-clamp recordings, surface biotinylation assays, and single-particle cryo-electron microscopy. Cryo-electron microscopy structural analysis of mBEST1-BF revealed closed and partially open conformations. Comparative analysis with human and chicken BEST1 orthologs highlighted conserved calcium-binding and gating mechanisms, with distinct features in mBEST1, including a wider aperture sufficient to accommodate dehydrated Cl ions and potential anion-binding sites near Val205 and Gln208 residues. The disordered C-terminal region of mBEST1 remains unresolved, suggesting it may require stabilizing factors for structural determination. Additionally, the autoinhibitory domain, which includes Ser354, likely plays a key role in regulating gating, with Ser354 potentially serving as a phosphorylation site that modulates channel activity. Our findings provide structural and functional insights into mBEST1 and suggest mechanisms underlying its unique gating and ion permeation properties.
History
DepositionNov 1, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62247.png

Downloads & links

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Map

FileDownload / File: emd_62247.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.2373786 - 7.4385324
Average (Standard dev.)-0.00027612015 (±0.23992765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62247_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_62247_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 : Docked Pentameric structure of mouse bestrophin-1 in a closed state

EntireName: Docked Pentameric structure of mouse bestrophin-1 in a closed state
Components
  • Complex: Docked Pentameric structure of mouse bestrophin-1 in a closed state
    • Protein or peptide: Bestrophin-1,Soluble cytochrome b562
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION

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Supramolecule #1: Docked Pentameric structure of mouse bestrophin-1 in a closed state

SupramoleculeName: Docked Pentameric structure of mouse bestrophin-1 in a closed state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Bestrophin-1,Soluble cytochrome b562

MacromoleculeName: Bestrophin-1,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 79.285266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTITYTNKVA NARLGSFSSL LLCWRGSIYK LLYGEFLVFI FLYYSIRGLY RMVLSSDQQL LFEKLALYCD SYIQLIPISF VLGFYVTLV VSRWWSQYEN LPWPDRLMIQ VSSFVEGKDE EGRLLRRTLI RYAILGQVLI LRSISTSVYK RFPTLHHLVL A GFMTHGEH ...String:
MTITYTNKVA NARLGSFSSL LLCWRGSIYK LLYGEFLVFI FLYYSIRGLY RMVLSSDQQL LFEKLALYCD SYIQLIPISF VLGFYVTLV VSRWWSQYEN LPWPDRLMIQ VSSFVEGKDE EGRLLRRTLI RYAILGQVLI LRSISTSVYK RFPTLHHLVL A GFMTHGEH KQLQKLGLPH NTFWVPWVWF ANLSMKAYLG GRIRDTVLLQ SLMNEVCTLR TQCGQLYAYD WISIPLVYTQ VV TVAVYSF FLACLIGRQF LNPNKDYPGH EMDLVVPVFT ILQFLFYMGW LKVAEQLINP FGEDDDDFET NWIIDRNLQV SLL SVDGMH QNLPPMERDM YWNEAAPQPP YTAASARSRR HSFMGSTFNI SLKKEDLELW SKEEADTDKK ESGYSSTIGC FLGL QPKNY HLPLKDLKTK LLCSKNPLLE GQCKDANQKN QKDVWKFKGL DFLKCVPRFK RRGSHCGPQA PSSHPTEQSA PSSSD TGDG PSTDYQEICH MKKKTVEFNL NIPESPTEHL QQRRLDQMST NIQALMKEHA ESYPYRDEAG TKPVLYETGL EVLFQG PAD LEDNWETLND NLKVIEKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLA NE GKVKEAQAAA EQLKTTRNAY IQKYLDYKDH DGDYKDHDID YKDDDDK

UniProtKB: Bestrophin-1, Soluble cytochrome b562

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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: 10 / Formula: CL
Molecular weightTheoretical: 35.453 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39144
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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