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- PDB-9bgu: Cryo-EM structure of Trypanosoma cruzi MscS G63V in lipid nanodiscs -

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Basic information

Entry
Database: PDB / ID: 9bgu
TitleCryo-EM structure of Trypanosoma cruzi MscS G63V in lipid nanodiscs
ComponentsMechanosensitive ion channel MscS domain-containing protein
KeywordsTRANSPORT PROTEIN / ion channels / mechanosensitive channels / membrane protein / heptameric
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsZhang, J. / Yuan, P.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mechanosensitive ion channel MscS domain-containing protein
B: Mechanosensitive ion channel MscS domain-containing protein
C: Mechanosensitive ion channel MscS domain-containing protein
D: Mechanosensitive ion channel MscS domain-containing protein
E: Mechanosensitive ion channel MscS domain-containing protein
F: Mechanosensitive ion channel MscS domain-containing protein
G: Mechanosensitive ion channel MscS domain-containing protein


Theoretical massNumber of molelcules
Total (without water)131,9187
Polymers131,9187
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "D"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "A"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 137 / Label seq-ID: 1 - 137

Dom-IDAuth asym-IDLabel asym-ID
d_1DD
d_2BB
d_3CC
d_4AA
d_5EE
d_6FF
d_7GG

NCS oper:
IDCodeMatrixVector
1given(-0.222521192664, 0.974927853133, 6.74895980828E-7), (-0.974927853133, -0.222521192664, -5.37481412118E-8), (9.77780986567E-8, -6.69934990163E-7, 1)28.5226571246, 253.146143229, 8.06060086518E-5
2given(0.623490537557, 0.781830895768, 6.9887739719E-7), (-0.781830895768, 0.623490537556, 3.41947374008E-7), (-1.68398422334E-7, -7.59604893514E-7, 1)-46.6930954809, 133.440758509, 0.000122834360241
3given(-0.900969675244, 0.433882062652, 5.11208191569E-7), (-0.433882062652, -0.900969675244, -1.0534147541E-7), (4.14877301706E-7, -3.16713539492E-7, 1)169.008466816, 268.974960911, -3.3959195207E-6
4given(0.623490585823, -0.781830857276, -1.27906939608E-6), (0.781830857277, 0.623490585823, 5.83294021642E-7), (3.41450462086E-7, -1.36369425371E-6, 0.999999999999)133.440979882, -46.6931244678, 0.000148045397196
5given(-0.222520084339, -0.9749281061, -9.23699319325E-7), (0.974928106101, -0.222520084339, -8.0956309937E-7), (5.83724168798E-7, -1.08068447715E-6, 0.999999999999)253.146168148, 28.5226944078, 8.20687118335E-5
6given(-0.900967964274, -0.433885615517, -7.62973743652E-8), (0.433885615517, -0.900967964274, -3.32210055093E-7), (7.53996741737E-8, -3.32414950287E-7, 1)268.975192122, 169.007920338, 3.69693878497E-5

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Components

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


Mass: 18845.473 Da / Num. of mol.: 7 / Mutation: G63V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: ECC02_000513 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A7J6YIJ5
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TcMscS G63V in nanodiscs / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Trypanosoma cruzi (eukaryote)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl PH 8.0, 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMTrisTris1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 42.16 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 3145

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Processing

EM software
IDNameVersionCategory
7Coot0.9.6model fitting
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2026538
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187037 / Symmetry type: POINT
Atomic model buildingPDB-ID: 9BGQ

9bgq


Accession code: 9BGQ / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 55.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00147357
ELECTRON MICROSCOPYf_angle_d0.302110003
ELECTRON MICROSCOPYf_chiral_restr0.03671211
ELECTRON MICROSCOPYf_plane_restr0.0021253
ELECTRON MICROSCOPYf_dihedral_angle_d2.26111022
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DDELECTRON MICROSCOPYNCS constraints2.67299868445E-12
ens_1d_3DDELECTRON MICROSCOPYNCS constraints1.85043279134E-13
ens_1d_4DDELECTRON MICROSCOPYNCS constraints4.64654041025E-13
ens_1d_5DDELECTRON MICROSCOPYNCS constraints1.00501176035E-11
ens_1d_6DDELECTRON MICROSCOPYNCS constraints3.30017076191E-12
ens_1d_7DDELECTRON MICROSCOPYNCS constraints1.29910398515E-12

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