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- PDB-28ob: Closed state Escherichia coli MscL mechanosensitive channel in DO... -

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Basic information

Entry
Database: PDB / ID: 28ob
TitleClosed state Escherichia coli MscL mechanosensitive channel in DOPC nanodiscs
ComponentsLarge-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / Mechanosensitive / large conductance / ion channel / MscL / Escherichia coli
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: 4.38 Å
AuthorsHardman, K. / Pliotas, C.
Funding support United Kingdom, 1items
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, J.L. / Waheed, Q. / Liu, X. / Arul, D. / Porav, S.A. / Calabrese, A.N. / Muench, S.P. / Pliotas, C.
History
DepositionFeb 10, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large-conductance mechanosensitive channel
C: Large-conductance mechanosensitive channel
D: Large-conductance mechanosensitive channel
E: Large-conductance mechanosensitive channel
B: 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
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mscL, yhdC, b3291, JW3252 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 complex of Escherichia coli MscL / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMSodium phosphateNa3PO41
2300 mMSodium chlorideNaCl1
SpecimenConc.: 1 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 R2/2
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: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 43 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7095
EM imaging opticsEnergyfilter name: TFS Selectris X

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPUimage acquisition
4CTFFINDCTF correction
7Coot0.9.8.96model fitting
9PHENIX1.17.1_3660model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionDetails: CTFFIND 4.0 in RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52307 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Chain-ID: A / Pdb chain-ID: A / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeChain residue rangeDetails (eV)Initial refinement model-IDPdb chain residue range
14LKU

4lku

4LKU108-136EcMscL CTD1108-136
22OAR

2oar

2OAR1-102MtMscL TMD21-102
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035070
ELECTRON MICROSCOPYf_angle_d0.6056830
ELECTRON MICROSCOPYf_dihedral_angle_d38.321670
ELECTRON MICROSCOPYf_chiral_restr0.039820
ELECTRON MICROSCOPYf_plane_restr0.004860

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