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- EMDB-56663: Closed state Escherichia coli MscL mechanosensitive channel in DM... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56663
TitleClosed state Escherichia coli MscL mechanosensitive channel in DMPC nanodiscs
Map data> map sharpened using cryoSPARC > "Hide Dust" tool at a threshold of 17.32 used in ChimeraX to remove nanodisc/lipid density
Sample
  • Complex: Pentameric complex of Escherichia coli MscL
    • Protein or peptide: Large-conductance mechanosensitive channel
KeywordsMechanosensitive / large conductance / ion channel / MscL / Escherichia coli / 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: 4.1 Å
AuthorsHardman K / Pliotas C
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S018069/1 United Kingdom
CitationJournal: Nat Comm / Year: 2026
Title: Structural basis of the gating mechanism of the large-conductance mechanosensitive channel from Escherichia coli
Authors: Hardman K / Wort JL / Waheed Q / Liu X / Arul D / Porav SA / Calabrese AN / Muench SP / Pliotas C
History
DepositionFeb 10, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56663.png

Downloads & links

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Map

FileDownload / File: emd_56663.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation> map sharpened using cryoSPARC > "Hide Dust" tool at a threshold of 17.32 used in ChimeraX to remove nanodisc/lipid density
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 324 pix.
= 266.328 Å		0.82 Å/pix.
x 324 pix.
= 266.328 Å		0.82 Å/pix.
x 324 pix.
= 266.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.48173752 - 0.7801859
Average (Standard dev.)0.0001320529 (±0.015525224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 266.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56663_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: > unsharpened CryoSPARC map

Fileemd_56663_additional_1.map
Annotation> unsharpened CryoSPARC map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56663_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56663_half_map_2.map
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 complex of Escherichia coli MscL

EntireName: Pentameric complex of Escherichia coli MscL
Components
  • Complex: Pentameric complex of Escherichia coli MscL
    • Protein or peptide: Large-conductance mechanosensitive channel

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Supramolecule #1: Pentameric complex of Escherichia coli MscL

SupramoleculeName: Pentameric complex of Escherichia coli MscL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Large-conductance mechanosensitive channel

MacromoleculeName: Large-conductance mechanosensitive channel / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.801593 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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
50.0 mMNa3PO4Sodium phosphate
300.0 mMNaClSodium chloride
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 1e-05 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 13105 / Average electron dose: 43.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 96000
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

CTF correctionSoftware - Name: cryoSPARC / Details: Patch CTF in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2oar

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 121887
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

4lku

chain_id: A, residue_range: 108-136, source_name: PDB, initial_model_type: experimental modelEcMscL CTD

2oar

chain_id: A, residue_range: 1-102, source_name: PDB, initial_model_type: experimental modelMtMscL TMD
RefinementProtocol: RIGID BODY FIT
Output model

PDB-28oa:
Closed state Escherichia coli MscL mechanosensitive channel in DMPC nanodiscs

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