[English] 日本語
Yorodumi
- EMDB-62483: Cryo-EM structure of mouse bestrophin-1 in a closed state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62483
TitleCryo-EM structure of mouse bestrophin-1 in a closed state
Map data
Sample
  • Complex: Pentameric structure of mouse bestrophin-1 in a closed state
    • Protein or peptide: Bestrophin-1,Soluble cytochrome b562
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION
KeywordsClosed / Calcium-bound / 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 / ligand-gated channel activity / intracellularly calcium-gated chloride channel activity / Stimuli-sensing channels / glutamate secretion / chloride transport ...membrane microdomain / bicarbonate channel activity / transepithelial chloride transport / gamma-aminobutyric acid secretion, neurotransmission / detection of light stimulus involved in visual perception / ligand-gated channel activity / intracellularly calcium-gated chloride channel activity / 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)
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 22, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62483.png

Downloads & links

-
Map

FileDownload / File: emd_62483.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-4.541321 - 7.2627816
Average (Standard dev.)-0.0009695165 (±0.23389426)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_62483_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62483_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

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

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

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

SupramoleculeName: 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)

-
Macromolecule #1: Bestrophin-1,Soluble cytochrome b562

MacromoleculeName: Bestrophin-1,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Details: BRIL and 3X FLAG / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
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

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 10 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
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: 29698
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • 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.
  • 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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more