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- PDB-28yc: pentameric MscL from Escherichia coli in nanodiscs -

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Basic information

Entry
Database: PDB / ID: 28yc
Titlepentameric MscL from Escherichia coli in nanodiscs
ComponentsLarge-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / mechanosensitive channel / bacteria / osmotic shock
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / monoatomic ion transport / monoatomic ion transmembrane transport / membrane / identical protein binding / plasma membrane
Similarity search - Function
Large-conductance mechanosensitive channel / Large-conductance mechanosensitive channel, conserved site / Large-conductance mechanosensitive channels mscL family signature. / Large-conductance mechanosensitive channel MscL / Large-conductance mechanosensitive channel/anditomin synthesis protein L / Large-conductance mechanosensitive channel, MscL
Similarity search - Domain/homology
Large-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsRasmussen, T. / Flegler, V.J. / Bottcher, B.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)456578072 Germany
German Research Foundation (DFG)525040890 Germany
CitationJournal: J Mol Biol / Year: 2026
Title: The Structure of Escherichia coli MscL and Its Dimer Formation in Nanodiscs.
Authors: Tim Rasmussen / Julia Isabel Bahner / Vanessa J Flegler / Tamsanqa T Hove / Christian Kraft / Akiko Rasmussen / Bettina Böttcher /
Abstract: Mechanosensitive channels of large conductance (MscL) are essential bacterial safety valves that prevent osmotic lysis by releasing solutes in response to membrane tension. Despite extensive ...Mechanosensitive channels of large conductance (MscL) are essential bacterial safety valves that prevent osmotic lysis by releasing solutes in response to membrane tension. Despite extensive functional studies on Escherichia coli MscL (EcMscL), its high-resolution structure remained unknown. Using cryo-electron microscopy, we present an experimental structure of EcMscL reconstituted in nanodiscs at 3.1 Å resolution. The structure reveals a pentameric assembly with a narrow hydrophobic gate at the cytosolic side and a periplasmic cavity, consistent with the canonical MscL-fold. Differences to earlier published crystal structures of MscL from other organisms are in the less conserved periplasmic loop. We observe a previously unreported dimeric association of EcMscL pentamers, mediated by residues 61-63 in the periplasmic loop. This dimeric interface is located at the periplasmic side and provides a structural basis for the formation of higher-order clusters. The observed arrangement enables a fluid-like, mosaic packing of channels with centre-to-centre distances of 5.9-9 nm, consistent with biophysical and imaging data. These findings provide a structural framework for understanding cluster organisation of EcMscL that modulates its activity in cellular stress response.
History
DepositionFeb 27, 2026Deposition 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

Downloads & links

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Assembly

Deposited unit
A: Large-conductance mechanosensitive channel
B: Large-conductance mechanosensitive channel
C: Large-conductance mechanosensitive channel
D: Large-conductance mechanosensitive channel
E: Large-conductance mechanosensitive channel


Theoretical massNumber of molelcules
Total (without water)79,0085
Polymers79,0085
Non-polymers00
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
Large-conductance mechanosensitive channel


Mass: 15801.593 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: C-terminal His6-tag / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mscL, yhdC, b3291, JW3252 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A742
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: pentameric MscL in nanodiscs MSP1E3D1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.075 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 1 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 R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K / Details: 5 sec at blot force +20

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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: 5.89 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: 14428
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 5 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPU3.8image acquisition
4cryoSPARC4.7CTF correction
7Coot0.9.8.93model fitting
9cryoSPARC4.7initial Euler assignment
10cryoSPARC4.7final Euler assignment
12cryoSPARC4.73D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3052300
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121943 / Symmetry type: POINT
Atomic model buildingB value: 123 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation
Atomic model buildingDetails: Modelangelo / Source name: Other / Type: other
RefinementHighest resolution: 3.12 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033810
ELECTRON MICROSCOPYf_angle_d0.4825130
ELECTRON MICROSCOPYf_dihedral_angle_d4.053500
ELECTRON MICROSCOPYf_chiral_restr0.04625
ELECTRON MICROSCOPYf_plane_restr0.006630

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