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- PDB-9bgq: Cryo-EM structure of Trypanosoma cruzi MscS -

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Basic information

Entry
Database: PDB / ID: 9bgq
TitleCryo-EM structure of Trypanosoma cruzi MscS
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: 3.21 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: Additional map / Part number: 2 / 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

Downloads & links

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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)131,6247
Polymers131,6247
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 "F"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "A"
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_1FF
d_2BB
d_3CC
d_4DD
d_5EE
d_6AA
d_7GG

NCS oper:
IDCodeMatrixVector
1given(-0.900967451161, 0.433886680998, -7.73355831299E-7), (-0.433886680999, -0.900967451161, 8.02075528776E-7), (-3.48758543075E-7, 1.05819273967E-6, 0.999999999999)169.007853103, 268.975158474, -6.2961235372E-5
2given(-0.900969108478, -0.433883239557, -1.48552945163E-7), (0.433883239557, -0.900969108478, -7.18451074465E-7), (1.77882265087E-7, -7.11756857139E-7, 1)268.975030465, 169.008331909, 4.84363229134E-5
3given(-0.222522854758, -0.974927473769, 7.93963475091E-7), (0.974927473769, -0.222522854758, 7.14371294784E-8), (1.07028998875E-7, 7.89953199023E-7, 1)253.146211782, 28.5229451463, -8.64462563754E-5
4given(0.623487908189, -0.781832992615, 8.8177697043E-7), (0.781832992615, 0.623487908189, -3.94478396203E-7), (-2.41361053757E-7, 9.35354837685E-7, 1)133.441242917, -46.6929487824, -6.28367989748E-5
5given(-0.222519436547, 0.974928253955, -4.31671170526E-7), (-0.974928253955, -0.222519436547, -2.77132172067E-8), (-1.23073624102E-7, 4.14681691086E-7, 1)28.5225594711, 253.146020843, -2.61329635407E-5
6given(0.623491238502, 0.781830336781, -2.95850516409E-8), (-0.781830336781, 0.623491238501, -5.25209301937E-7), (-3.92178544925E-7, 3.50593889025E-7, 1)-46.6930622007, 133.440747736, 8.84124101219E-6

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Components

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


Mass: 18803.393 Da / Num. of mol.: 7
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 / Type: COMPLEX / Details: TcMscS in GDN / 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 and 0.04 mM GDN
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMTrisTris1
30.04 mMglyco-diosgeninGDN1
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: 43.11 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 3269

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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: 2193852
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229377 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 59.91 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00157364
ELECTRON MICROSCOPYf_angle_d0.340910003
ELECTRON MICROSCOPYf_chiral_restr0.03731197
ELECTRON MICROSCOPYf_plane_restr0.00261260
ELECTRON MICROSCOPYf_dihedral_angle_d2.57751022
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FFELECTRON MICROSCOPYNCS constraints5.39456713997E-13
ens_1d_3FFELECTRON MICROSCOPYNCS constraints8.21009540576E-13
ens_1d_4FFELECTRON MICROSCOPYNCS constraints2.2184596994E-13
ens_1d_5FFELECTRON MICROSCOPYNCS constraints1.49999813983E-13
ens_1d_6FFELECTRON MICROSCOPYNCS constraints2.57602410846E-12
ens_1d_7FFELECTRON MICROSCOPYNCS constraints2.04680186679E-13

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