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- EMDB-12996: Mechanosensitive channel MscS solubilized with LMNG in open confo... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12996 | |||||||||
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Title | Mechanosensitive channel MscS solubilized with LMNG in open conformation | |||||||||
![]() | post-processed map, un-masked, sharpened B = -50, cropped box 256 pix | |||||||||
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![]() | mechanosensitive channel / LMNG stack / delipidation / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
![]() | Rasmussen T / Flegler VJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanosensitive channel gating by delipidation. Authors: Vanessa Judith Flegler / Akiko Rasmussen / Karina Borbil / Lea Boten / Hsuan-Ai Chen / Hanna Deinlein / Julia Halang / Kristin Hellmanzik / Jessica Löffler / Vanessa Schmidt / Cihan Makbul ...Authors: Vanessa Judith Flegler / Akiko Rasmussen / Karina Borbil / Lea Boten / Hsuan-Ai Chen / Hanna Deinlein / Julia Halang / Kristin Hellmanzik / Jessica Löffler / Vanessa Schmidt / Cihan Makbul / Christian Kraft / Rainer Hedrich / Tim Rasmussen / Bettina Böttcher / ![]() Abstract: The mechanosensitive channel of small conductance (MscS) protects bacteria against hypoosmotic shock. It can sense the tension in the surrounding membrane and releases solutes if the pressure in the ...The mechanosensitive channel of small conductance (MscS) protects bacteria against hypoosmotic shock. It can sense the tension in the surrounding membrane and releases solutes if the pressure in the cell is getting too high. The membrane contacts MscS at sensor paddles, but lipids also leave the membrane and move along grooves between the paddles to reside as far as 15 Å away from the membrane in hydrophobic pockets. One sensing model suggests that a higher tension pulls lipids from the grooves back to the membrane, which triggers gating. However, it is still unclear to what degree this model accounts for sensing and what contribution the direct interaction of the membrane with the channel has. Here, we show that MscS opens when it is sufficiently delipidated by incubation with the detergent dodecyl-β-maltoside or the branched detergent lauryl maltose neopentyl glycol. After addition of detergent-solubilized lipids, it closes again. These results support the model that lipid extrusion causes gating: Lipids are slowly removed from the grooves and pockets by the incubation with detergent, which triggers opening. Addition of lipids in micelles allows lipids to migrate back into the pockets, which closes the channel even in the absence of a membrane. Based on the distribution of the aliphatic chains in the open and closed conformation, we propose that during gating, lipids leave the complex on the cytosolic leaflet at the height of highest lateral tension, while on the periplasmic side, lipids flow into gaps, which open between transmembrane helices. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.7 KB 20.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.9 KB | Display | ![]() |
Images | ![]() | 163.9 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7onjMC ![]() 7onlC ![]() 7oo0C ![]() 7oo6C ![]() 7oo8C ![]() 7ooaC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | post-processed map, un-masked, sharpened B = -50, cropped box 256 pix | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0635 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half-map, cropped to 256 pix
File | emd_12996_half_map_1.map | ||||||||||||
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Annotation | half-map, cropped to 256 pix | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map, cropped to 256 pix
File | emd_12996_half_map_2.map | ||||||||||||
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Annotation | half-map, cropped to 256 pix | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : homoheptameric complex of MscS coordinated with lipids and deterg...
Entire | Name: homoheptameric complex of MscS coordinated with lipids and detergents DDM and LMNG |
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Components |
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-Supramolecule #1: homoheptameric complex of MscS coordinated with lipids and deterg...
Supramolecule | Name: homoheptameric complex of MscS coordinated with lipids and detergents DDM and LMNG type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 224 KDa |
-Macromolecule #1: Mechanosensitive channel of small conductance (MscS)
Macromolecule | Name: Mechanosensitive channel of small conductance (MscS) / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 31.994039 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEDLNVVDSI NGAGSWLVAN QALLLSYAVN IVAALAIIIV GLIIARMISN AVNRLMISRK IDATVADFLS ALVRYGIIAF TLIAALGRV GVQTASVIAV LGAAGLAVGL ALQGSLSNLA AGVLLVMFRP FRAGEYVDLG GVAGTVLSVQ IFSTTMRTAD G KIIVIPNG ...String: MEDLNVVDSI NGAGSWLVAN QALLLSYAVN IVAALAIIIV GLIIARMISN AVNRLMISRK IDATVADFLS ALVRYGIIAF TLIAALGRV GVQTASVIAV LGAAGLAVGL ALQGSLSNLA AGVLLVMFRP FRAGEYVDLG GVAGTVLSVQ IFSTTMRTAD G KIIVIPNG KIIAGNIINF SREPVRRNEF IIGVAYDSDI DQVKQILTNI IQSEDRILKD REMTVRLNEL GASSINFVVR VW SNSGDLQ NVYWDVLERI KREFDAAGIS FPYPQMDVNF KRVKEDKAAL EHHHHHH UniProtKB: Uncharacterized protein |
-Macromolecule #2: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Macromolecule | Name: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 2 / Number of copies: 7 / Formula: PEE |
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Molecular weight | Theoretical: 744.034 Da |
Chemical component information | ![]() ChemComp-PEE: |
-Macromolecule #3: DODECYL-BETA-D-MALTOSIDE
Macromolecule | Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 3 / Number of copies: 21 / Formula: LMT |
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Molecular weight | Theoretical: 510.615 Da |
Chemical component information | ![]() ChemComp-LMT: |
-Macromolecule #4: Lauryl Maltose Neopentyl Glycol
Macromolecule | Name: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 4 / Number of copies: 35 / Formula: AV0 |
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Molecular weight | Theoretical: 1.005188 KDa |
Chemical component information | ![]() ChemComp-AV0: |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 266 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 7 sec blotting, blot force +25. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3292 / Average exposure time: 75.0 sec. / Average electron dose: 78.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 52 / Target criteria: WEIGHTED MAP SUM AT ATOM CENTERS |
Output model | ![]() PDB-7onj: |