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- EMDB-44520: Cryo-EM structure of Trypanosoma cruzi MscS -

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Basic information

Entry
Database: EMDB / ID: EMD-44520
TitleCryo-EM structure of Trypanosoma cruzi MscS
Map datasharp
Sample
  • Complex: TcMscS
    • 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: 3.21 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: 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, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44520.png

Downloads & links

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Map

FileDownload / File: emd_44520.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-5.5852075 - 11.173448
Average (Standard dev.)0.00793564 (±0.25296447)
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: deepEMhancer

Fileemd_44520_additional_1.map
AnnotationdeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: map

Fileemd_44520_additional_2.map
Annotationmap
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_44520_half_map_1.map
Annotationhalf_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_44520_half_map_2.map
Annotationhalf_B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TcMscS

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

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Supramolecule #1: TcMscS

SupramoleculeName: TcMscS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: TcMscS in GDN
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
0.04 mMGDNglyco-diosgenin

Details: 20 mM Tris-HCl PH 8.0, 150 mM NaCl and 0.04 mM GDN
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: 3269 / Average electron dose: 43.11 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: 2193852
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229377
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

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

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