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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: To Be Published
Title: Lipid-mediated gating of a miniature mechanosensitive MscS channel from Trypanosoma cruzi
Authors: Zhang, J. / Bhatt, A. / Maksaev, G. / Luo, Y. / Yuan, P.
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

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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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