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- EMDB-52344: Cryo-EM structure of bovine TMEM206 -

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Basic information

Entry
Database: EMDB / ID: EMD-52344
TitleCryo-EM structure of bovine TMEM206
Map data
Sample
  • Complex: Bos taurus Proton-activated chloride channel with C-terminal venus GFP
    • Protein or peptide: Proton-activated chloride channel
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsChloride channel gated by pH that facilitates the entry of chloride ions into cells upon exposure to extracellular acidic pH / 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: 2.86 Å
AuthorsBrunner JD / Schenck S / De Gieter S
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: Gangadhar Eluru / Steven De Gieter / Stephan Schenck / Annelore Stroobants / Binesh Shrestha / Paul Erbel / Janine D Brunner / Rouslan G Efremov /
Abstract: Single-particle cryogenic electron microscopy (cryo-EM) enables reconstruction of atomic-resolution 3D maps of proteins by visualizing thousands to millions of purified protein particles embedded in ...Single-particle cryogenic electron microscopy (cryo-EM) enables reconstruction of atomic-resolution 3D maps of proteins by visualizing thousands to millions of purified protein particles embedded in vitreous ice. This corresponds to picograms of purified protein, which can potentially be isolated from a few thousand cells. Hence, cryo-EM holds the potential of a very sensitive analytical method for delivering high-resolution protein structure as a readout. In practice, millions of times more starting biological material is required to prepare cryo-EM grids. Here we show that using a micro isolation (MISO) method, which combines microfluidics-based protein purification with cryo-EM grid preparation, cryo-EM structures of soluble bacterial and eukaryotic membrane proteins can be solved starting from less than 1 µg of a target protein and progressing from cells to cryo-EM grids within a few hours. This scales down the amount of starting biological material hundreds to thousands of times, opening possibilities for the structural characterization of hitherto inaccessible proteins.
History
DepositionDec 16, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52344.png

Downloads & links

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Map

FileDownload / File: emd_52344.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 400 pix.
= 304. Å		0.76 Å/pix.
x 400 pix.
= 304. Å		0.76 Å/pix.
x 400 pix.
= 304. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-1.5847231 - 1.8555504
Average (Standard dev.)-0.0001800264 (±0.023307355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52344_msk_1.map
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Half map: #2

Fileemd_52344_half_map_1.map
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Half map: #1

Fileemd_52344_half_map_2.map
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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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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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: #1
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: 40.180898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIRQELSTSY QELSEELDQV VENSEQADER DKETVKVHGP GILPALDSES ASSSIRFSKA CLKNVFSVLL IFIYLLLMAV AVFLVYQTI MDFREKLKHP VMSVSYKEVD RYDAPGIALY PGQAQLLSCK HYYEVIPPLR SPGQPGDVNC TTQRVNYTDP F SNQTLKSA ...String:
MIRQELSTSY QELSEELDQV VENSEQADER DKETVKVHGP GILPALDSES ASSSIRFSKA CLKNVFSVLL IFIYLLLMAV AVFLVYQTI MDFREKLKHP VMSVSYKEVD RYDAPGIALY PGQAQLLSCK HYYEVIPPLR SPGQPGDVNC TTQRVNYTDP F SNQTLKSA LIVRGPREVQ KRELVFLQFR LNQSSEDFSA IDYLLFSSFQ EFLQSPDRAG FMQACESAYS SWKFSGGFRT WV KMSLVET KEEDGREAVE FRQETSVVNY IDQRPAAEKS AQLFFVVFEW KDPFIQKVQD IITANPWNTI ALLCGAFLAL FKA AEFAKL SVKWMIKIRR RYLKKRGQAT NHIS

UniProtKB: Proton-activated chloride channel

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 29 / 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
Details: 150 mM NaCl, 30 mM HEPES-Na, pH 7.6, 0.0063% GDN, 10 mM D-(+)-biotin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: LEICA EM GP

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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: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 332041
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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