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- PDB-9sdt: mechanosensitive channel MscS from Francisella tularensis in DM -

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Basic information

Entry
Database: PDB / ID: 9sdt
Titlemechanosensitive channel MscS from Francisella tularensis in DM
ComponentsSmall-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / mechanosensitive channel / lipid interaction / bacteria
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
TETRADECANE / DECANE / DODECANE / N-OCTANE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsRasmussen, A. / Hemmelmann, N. / Hove, T.T. / Flegler, V.J. / Rasmussen, T. / Bottcher, B.
Funding support Germany, 4items
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, T.T. / Flegler, V.J. / Kraft, C. / Hedrich, R. / Rasmussen, T. / Bottcher, B.
History
DepositionAug 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small-conductance mechanosensitive channel
B: Small-conductance mechanosensitive channel
C: Small-conductance mechanosensitive channel
D: Small-conductance mechanosensitive channel
E: Small-conductance mechanosensitive channel
F: Small-conductance mechanosensitive channel
G: Small-conductance mechanosensitive channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,77070
Polymers130,6127
Non-polymers14,15863
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 7 molecules ABCDEFG

#1: Protein
Small-conductance mechanosensitive channel


Mass: 18658.873 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: C-terminal His6-tag / Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: FWI86_02060, FWJ04_01320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B3VCY4

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Non-polymers , 5 types, 63 molecules

#2: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C8H18 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C14H30 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#6: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: homoheptameric complex of detergent solubilised MscS / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)Organism: Francisella tularensis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
30.15 %DMC22H42O111
45 mMEDTAC10H16N2O81
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.06 sec. / Electron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9222
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 5 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPU3.7.0image acquisition
4cryoSPARC4.7CTF correction
7Coot0.9.8.93model fitting
9cryoSPARC4.7initial Euler assignment
10cryoSPARC4.7final Euler assignment
11cryoSPARC4.7classification
12cryoSPARC4.73D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1950485
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 336790 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 12 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 6RLD

6rld


Accession code: 6RLD / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039289
ELECTRON MICROSCOPYf_angle_d0.5312292
ELECTRON MICROSCOPYf_dihedral_angle_d5.3751813
ELECTRON MICROSCOPYf_chiral_restr0.0411470
ELECTRON MICROSCOPYf_plane_restr0.0021400

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