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- EMDB-56958: pentameric MscL from Escherichia coli in nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-56958
Titlepentameric MscL from Escherichia coli in nanodiscs
Map datasharpened map in phenix: -50
Sample
  • Complex: pentameric MscL in nanodiscs MSP1E3D1
    • Protein or peptide: Large-conductance mechanosensitive channel
Keywordsmechanosensitive channel / bacteria / osmotic shock / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsRasmussen T / Flegler VJ / Bottcher B
Funding support Germany, 3 items
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, 2026-
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_56958.png

Downloads & links

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Map

FileDownload / File: emd_56958.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map in phenix: -50
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 7.0
Minimum - Maximum-27.548425999999999 - 48.560630000000003
Average (Standard dev.)0.000000000011037 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: half map A

Fileemd_56958_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_56958_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pentameric MscL in nanodiscs MSP1E3D1

EntireName: pentameric MscL in nanodiscs MSP1E3D1
Components
  • Complex: pentameric MscL in nanodiscs MSP1E3D1
    • Protein or peptide: Large-conductance mechanosensitive channel

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Supramolecule #1: pentameric MscL in nanodiscs MSP1E3D1

SupramoleculeName: pentameric MscL in nanodiscs MSP1E3D1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 75 KDa

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Macromolecule #1: Large-conductance mechanosensitive channel

MacromoleculeName: Large-conductance mechanosensitive channel / type: protein_or_peptide / ID: 1 / Details: C-terminal His6-tag / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.801593 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSIIKEFREF AMRGNVVDLA VGVIIGAAFG KIVSSLVADI IMPPLGLLIG GIDFKQFAVT LRDAQGDIPA VVMHYGVFIQ NVFDFLIVA FAIFMAIKLI NKLNRKKEEP AAAPAPTKEE VLLTEIRDLL KEQNNRSHHH HHH

UniProtKB: Large-conductance mechanosensitive channel

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / 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 / Details: 5 sec at blot force +20.

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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: 14428 / Average exposure time: 5.89 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: 3052300
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 121943
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: Modelangelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 123 / Target criteria: Cross-correlation
Output model

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

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