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- EMDB-54785: mechanosensitive channel MscS from Francisella tularensis in DDM,... -

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Basic information

Entry
Database: EMDB / ID: EMD-54785
Titlemechanosensitive channel MscS from Francisella tularensis in DDM, asymmetric processing
Map datarefined in Relion and postprocessed with B=-50
Sample
  • Complex: homoheptameric complex of detergent solubilised MscS
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: N-OCTANE
  • Ligand: TETRADECANE
  • Ligand: DECANE
  • Ligand: DODECANE
Keywordsmechanosensitive channel / lipid interaction / 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: 2.8 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 13, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54785.png

Downloads & links

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Map

FileDownload / File: emd_54785.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined in Relion and postprocessed with B=-50
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 200 pix.
= 189.2 Å		0.95 Å/pix.
x 200 pix.
= 189.2 Å		0.95 Å/pix.
x 200 pix.
= 189.2 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: 0.0055
Minimum - Maximum-0.027452542 - 0.052757006
Average (Standard dev.)0.00009347406 (±0.001871675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 189.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_54785_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_54785_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 detergent solubilised MscS

EntireName: homoheptameric complex of detergent solubilised MscS
Components
  • Complex: homoheptameric complex of detergent solubilised MscS
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: N-OCTANE
  • Ligand: TETRADECANE
  • Ligand: DECANE
  • Ligand: DODECANE

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Supramolecule #1: homoheptameric complex of detergent solubilised MscS

SupramoleculeName: homoheptameric complex of detergent solubilised MscS / 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-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 2 / Number of copies: 7 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #3: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 3 / Number of copies: 12 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #4: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 4 / Number of copies: 17 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #5: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 5 / Number of copies: 13 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #6: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 6 / Number of copies: 13 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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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
50.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
0.15 %C24H46O11DDM
5.0 mMC10H16N2O8EDTA
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: 90 % / 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: 10734 / Average exposure time: 3.63 sec. / Average electron dose: 40.0 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: 1.4000000000000001 µm / Nominal defocus min: 0.6 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: 1995814
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 441953
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 5.0)
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 / Overall B value: 68
Output model

PDB-9sdg:
mechanosensitive channel MscS from Francisella tularensis in DDM, asymmetric processing

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