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- EMDB-54808: mechanosensitive channel MscS from Francisella tularensis in nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-54808
Titlemechanosensitive channel MscS from Francisella tularensis in nanodiscs
Map datalocal refinement, sharpened map in CryoSPARC with B = -110
Sample
  • Complex: homoheptameric complex of MscS in nanodiscs
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Keywordsmechanosensitive channel / osmotic stress / bacteria / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / plasma membrane
Similarity search - Function
Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / Mechanosensitive 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 / LSM domain superfamily
Similarity search - Domain/homology
Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRasmussen A / Hemmelmann N / Hove TT / Flegler VJ / Rasmussen T / Bottcher B
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)538122946 Germany
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)525040890 Germany
German Research Foundation (DFG)456578072 Germany
CitationJournal: To Be Published
Title: An asymmetric gate in the homoheptameric mechanosensitive channel MscS from Francisella tularensis
Authors: Rasmussen A / Hemmelmann N / Bahner J / Hove TT / Flegler VJ / Kraft C / Hedrich R / Rasmussen T / Bottcher B
History
DepositionAug 18, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54808.png

Downloads & links

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Map

FileDownload / File: emd_54808.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement, sharpened map in CryoSPARC with B = -110
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 242.176 Å		0.95 Å/pix.
x 256 pix.
= 242.176 Å		0.95 Å/pix.
x 256 pix.
= 242.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.8044953 - 1.1315217
Average (Standard dev.)0.001406493 (±0.028174961)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 242.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54808_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_54808_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_54808_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homoheptameric complex of MscS in nanodiscs

EntireName: homoheptameric complex of MscS in nanodiscs
Components
  • Complex: homoheptameric complex of MscS in nanodiscs
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: homoheptameric complex of MscS in nanodiscs

SupramoleculeName: homoheptameric complex of MscS in nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Francisella tularensis (bacteria)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Small-conductance mechanosensitive channel

MacromoleculeName: Small-conductance mechanosensitive channel / type: protein_or_peptide / ID: 1 / Details: C-terminal His6-tag / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Francisella tularensis (bacteria)
Molecular weightTheoretical: 18.658873 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MFDQLGNSGA FLINAIVAVV ILVVGFWASK YIKSIVYSLL KEYDKTVSQF LASLVYTIFL VLVVVIALAK LGVPISPVTG VLTGVVFGI SMSLKTSYNT VACGIMLAFS KPFEVGEKVD FGGIKGTVKS IGFLYTKLDD EDGNEIVISN NLVLSKVITR F TQTDKHHH HHH

UniProtKB: Small-conductance mechanosensitive channel

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Macromolecule #2: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 7 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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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

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3HClTris HCl
50.0 mMNaClsodium chloride
0.5 mMC10H14N2Na2O8EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.4 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 11589 / Average exposure time: 6.09 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2969169
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: map from related sample (MscS in detergent)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 70319
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6rld


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9sef:
mechanosensitive channel MscS from Francisella tularensis in nanodiscs

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