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- PDB-9p0n: MscS in Glyco-DIBMA Native Nanodiscs (C7 symmetry) -

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Basic information

Entry
Database: PDB / ID: 9p0n
TitleMscS in Glyco-DIBMA Native Nanodiscs (C7 symmetry)
ComponentsSmall-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / mechanosensitive channel / native nanodisc / polymer / Glyco-DIBMA / cryo-EM / lipid
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, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal ...Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / Mechanosensitive ion channel MscS, archaea/bacteria type / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / 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
Chem-D21 / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsMoller, E. / Britt, M. / Zhou, F. / Yang, H. / Anishkin, A. / Ernst, R. / Juan, V.M. / Sukharev, S. / Matthies, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)Z1A HD008998 United States
National Science Foundation (NSF, United States)DGE 1840340 United States
National Science Foundation (NSF, United States)CHE-1944892/2326678 United States
CitationJournal: bioRxiv / Year: 2025
Title: The lipid-mediated mechanism of mechanosensitive channel MscS inactivation.
Authors: Elissa Moller / Madolyn Britt / Fei Zhou / Hyojik Yang / Andriy Anishkin / Robert Ernst / Juan M Vanegas / Sergei Sukharev / Doreen Matthies
Abstract: Interpretations of experimental conformations of mechanosensitive channels gated by 'force from lipids' become more reliable when native lipids are preserved in the structures. MscS is an adaptive ...Interpretations of experimental conformations of mechanosensitive channels gated by 'force from lipids' become more reliable when native lipids are preserved in the structures. MscS is an adaptive osmolyte release valve that regulates turgor in osmotically stressed cells. MscS promptly opens under abrupt super-threshold tensions in the membrane, but at lower and more gradually applied tensions, it silently inactivates from the closed state. A central question has been whether to assign the commonly observed non-conductive conformation with splayed peripheral helices to a closed or inactivated state. We present a 3-Å MscS cryo-EM structure obtained in Glyco-DIBMA polymers, which avoid complete lipid removal. Within the complex, we observe densities for endogenous phospholipids intercalating between the peripheral and pore-lining helices. The lipidomic analysis shows a 2-3 fold enrichment of phosphatidylglycerol in Glyco-DIBMA-extracted MscS samples. The computed pressure of these lipids on the protein surface enforces the characteristic kinks in the pore-lining helices, sterically stabilizing the separation of the peripheral helices. Mutations of residues coordinating lipids in the crevices eliminate inactivation, allowing us to classify this group of structures as the inactivated state. Our study reveals a novel inactivation mechanism in which intercalated lipids physically decouple the tension-sensing helices from the gate.
History
DepositionJun 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 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: 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)241,16035
Polymers222,2627
Non-polymers18,89828
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Small-conductance mechanosensitive channel


Mass: 31751.768 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mscS, Z4261, ECs3795 / Plasmid: pB10d / Production host: Escherichia coli (E. coli) / Strain (production host): MJF465 / References: UniProt: P0C0S2
#2: Chemical...
ChemComp-D21 / (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate


Mass: 674.929 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C37H71O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
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: MscS in Glyco-DIBMA Native Nanodiscs (C7 symmetry) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.217 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: MJF465
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
2100 mMSodium Chloride1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / 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: 105000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 79 K / Temperature (min): 79 K
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20649
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv3.3.250particle selectionBlob Picker
2SerialEM4.1image acquisition
4cryoSPARCv3.3.250CTF correctionPatch CTF estimation (multi)
7Cootv.0.9.8.92model fitting
9PHENIXv.1.21.2-5419model refinement
10cryoSPARCv3.3.250initial Euler assignmentAb-Initio Reconstruction
11cryoSPARCv3.3.250final Euler assignmentNon-uniform Refinement (Legacy)
12cryoSPARCv3.3.250classification2D Classification
13cryoSPARCv3.3.2503D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3380588
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 368753 / Symmetry type: POINT
Atomic model buildingB value: 127.8 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7OO6

7oo6


Accession code: 7OO6 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.99 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215449
ELECTRON MICROSCOPYf_angle_d0.41920650
ELECTRON MICROSCOPYf_dihedral_angle_d11.8932968
ELECTRON MICROSCOPYf_chiral_restr0.0422401
ELECTRON MICROSCOPYf_plane_restr0.0032527

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