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

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Basic information

Entry
Database: PDB / ID: 9sef
Titlemechanosensitive channel MscS from Francisella tularensis in nanodiscs
ComponentsSmall-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / mechanosensitive channel / osmotic stress / 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
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 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)136,12214
Polymers130,6127
Non-polymers5,5107
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

#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
#2: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C44H85NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPC, phospholipid*YM
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 MscS in nanodiscs / 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
120 mMTris HClC4H11NO3HCl1
250 mMsodium chlorideNaCl1
30.5 mMEDTAC10H14N2Na2O81
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / 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: 500 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: 6.09 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: 11589
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 5 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPU3.8.1image 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: 2969169
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70319 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 6RLD

6rld


Accession code: 6RLD / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028575
ELECTRON MICROSCOPYf_angle_d0.34811606
ELECTRON MICROSCOPYf_dihedral_angle_d4.0631337
ELECTRON MICROSCOPYf_chiral_restr0.0391463
ELECTRON MICROSCOPYf_plane_restr0.0021351

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