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- EMDB-52345: Cryo-EM structure of bovine TMEM206-YFP purified and plunged usin... -

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Basic information

Entry
Database: EMDB / ID: EMD-52345
TitleCryo-EM structure of bovine TMEM206-YFP purified and plunged using MISO (micro-purification)
Map data
Sample
  • Complex: Bos taurus Proton-activated chloride channel with C-terminal venus GFP
    • Protein or peptide: Proton-activated chloride channel
KeywordspH-gated chloride channel / MEMBRANE PROTEIN
Function / homologypH-gated chloride channel activity / TMEM206 protein / TMEM206 protein family / chloride transport / chloride channel complex / plasma membrane / Proton-activated chloride channel
Function and homology information
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsDe Gieter S / Eluru G / Schenck S / Stroobants A / Efremov RG / Brunner JD
Funding support Belgium, European Union, 3 items
OrganizationGrant numberCountry
Other governmentG0H5916N
Research Foundation - Flanders (FWO)G054617N Belgium
European Research Council (ERC)726436European Union
CitationJournal: Nat.Methods / Year: 2025
Title: MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony
Authors: Eluru G / De Gieter S / Schenck S / Stroobants A / Shrestha B / Erbel P / Brunner JD / Efremov RG
History
DepositionDec 16, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52345.png

Downloads & links

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Map

FileDownload / File: emd_52345.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 200 pix.
= 278. Å		1.39 Å/pix.
x 200 pix.
= 278. Å		1.39 Å/pix.
x 200 pix.
= 278. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.315
Minimum - Maximum-2.5638433 - 3.2221053
Average (Standard dev.)0.0008707751 (±0.04919057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 278.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52345_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_52345_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52345_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Bos taurus Proton-activated chloride channel with C-terminal venus GFP

EntireName: Bos taurus Proton-activated chloride channel with C-terminal venus GFP
Components
  • Complex: Bos taurus Proton-activated chloride channel with C-terminal venus GFP
    • Protein or peptide: Proton-activated chloride channel

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Supramolecule #1: Bos taurus Proton-activated chloride channel with C-terminal venus GFP

SupramoleculeName: Bos taurus Proton-activated chloride channel with C-terminal venus GFP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Proton-activated chloride channel

MacromoleculeName: Proton-activated chloride channel / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 30.375881 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LLIFIYLLLM AVAVFLVYQT IMDFREKLKH PVMSVSYKEV DRYDAPGIAL YPGQAQLLSC KHYYEVIPPL RSPGQPGDVN CTTQRVNYT DPFSNQTLKS ALIVRGPREV QKRELVFLQF RLNQSSEDFS AIDYLLFSSF QEFLQSPDRA GFMQACESAY S SWKFSGGF ...String:
LLIFIYLLLM AVAVFLVYQT IMDFREKLKH PVMSVSYKEV DRYDAPGIAL YPGQAQLLSC KHYYEVIPPL RSPGQPGDVN CTTQRVNYT DPFSNQTLKS ALIVRGPREV QKRELVFLQF RLNQSSEDFS AIDYLLFSSF QEFLQSPDRA GFMQACESAY S SWKFSGGF RTWVKMSLVE TKEEDGREAV EFRQETSVVN YIDQRPAAEK SAQLFFVVFE WKDPFIQKVQ DIITANPWNT IA LLCGAFL ALFKAAEFAK LSVKWMA

UniProtKB: Proton-activated chloride channel

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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
Details: 150 mM NaCl, 30 mM HEPES-Na, pH 7.6, 0.0063% GDN, 10 mM D-(+)-biotin
GridModel: Au-flat 1.2/1.3 / Material: GOLD / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: HOMEMADE PLUNGER
Details: MISO Chip: 3 ul single column chip filled with Pierce High-capacity streptavidin agarose resin Plunging: 80 nl.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 87106
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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