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- EMDB-44521: Cryo-EM structure of Trypanosoma cruzi MscS in lipid nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-44521
TitleCryo-EM structure of Trypanosoma cruzi MscS in lipid nanodiscs
Map datasharp
Sample
  • Complex: TcMscS in nanodiscs
    • Protein or peptide: Mechanosensitive ion channel MscS domain-containing protein
Keywordsion channels / mechanosensitive channels / membrane protein / heptameric / TRANSPORT PROTEIN
Function / homologyMechanosensitive ion channel MscS, archaea/bacteria type / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / mechanosensitive monoatomic ion channel activity / LSM domain superfamily / membrane / Mechanosensitive ion channel MscS domain-containing protein
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsZhang J / Yuan P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143440 United States
CitationJournal: Nat Commun / Year: 2025
Title: Lipid-mediated gating of a miniature mechanosensitive MscS channel from Trypanosoma cruzi.
Authors: Jingying Zhang / Aashish Bhatt / Grigory Maksaev / Yun Lyna Luo / Peng Yuan /
Abstract: The mechanosensitive channel of small conductance (MscS) from E. coli (EcMscS) has served as the prevailing model system for understanding mechanotransduction in ion channels. Trypanosoma cruzi, the ...The mechanosensitive channel of small conductance (MscS) from E. coli (EcMscS) has served as the prevailing model system for understanding mechanotransduction in ion channels. Trypanosoma cruzi, the protozoan parasite causing Chagas disease, encodes a miniature MscS ortholog (TcMscS) critical for parasite development and infectivity. TcMscS contains a minimal portion of the canonical EcMscS fold yet maintains mechanosensitive channel activity, thus presenting a unique model system to assess the essential molecular determinants underlying mechanotransduction. Using cryo-electron microscopy and molecular dynamics simulations, we show that TcMscS contains two short membrane-embedded helices that would not fully cross an intact lipid bilayer. Consequently, drastic membrane deformation is induced at the protein-lipid interface, resulting in a funnel-shaped bilayer surrounding the channel. Resident lipids within the central pore lumen block ion permeation pathway, and their departure driven by lateral membrane tension is required for ion conduction. Together with electrophysiology and mutagenesis studies, our results support a direct lipid-mediated mechanical gating transition. Moreover, these findings provide a foundation for the development of alternative treatment of Chagas disease by inhibition of the TcMscS channel.
History
DepositionApr 19, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44521.png

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Map

FileDownload / File: emd_44521.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 192 pix.
= 230.4 Å		1.2 Å/pix.
x 192 pix.
= 230.4 Å		1.2 Å/pix.
x 192 pix.
= 230.4 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
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Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-5.2944336 - 8.631883
Average (Standard dev.)0.016628202 (±0.23905404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 230.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: map

Fileemd_44521_additional_1.map
Annotationmap
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Half map: half A

Fileemd_44521_half_map_1.map
Annotationhalf_A
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Half map: half B

Fileemd_44521_half_map_2.map
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Sample components

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Entire : TcMscS in nanodiscs

EntireName: TcMscS in nanodiscs
Components
  • Complex: TcMscS in nanodiscs
    • Protein or peptide: Mechanosensitive ion channel MscS domain-containing protein

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Supramolecule #1: TcMscS in nanodiscs

SupramoleculeName: TcMscS in nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma cruzi (eukaryote)

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Macromolecule #1: Mechanosensitive ion channel MscS domain-containing protein

MacromoleculeName: Mechanosensitive ion channel MscS domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma cruzi (eukaryote)
Molecular weightTheoretical: 18.803393 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString:
MKRFFNRFYL DTGIIADPSQ RSLASRVSAF LVQGAVAFSL LGTIGVDTSP LIAAAGVTGA TIGFACKDFG TNFVASIVLS GQQSIRTGN LVCIGTGLNV VKGKVVDWDT RYLYLRSSEG HLLHVPNNMV LNSVVTWEQE KKQNPHETDL PKQDVVKAPG D NAAKQSNS LEVLFQ

UniProtKB: Mechanosensitive ion channel MscS domain-containing protein

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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
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTrisTris

Details: 20 mM Tris-HCl PH 8.0, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 3956 / Average electron dose: 42.46 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm

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Image processing

Particle selectionNumber selected: 1467083
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9bgq

Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182063
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9bgq


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9bgs:
Cryo-EM structure of Trypanosoma cruzi MscS in lipid nanodiscs

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