[English] 日本語
Yorodumi- EMDB-4919: STRUCTURE OF THE MECHANOSENSITIVE CHANNEL MSCS EMBEDDED IN THE ME... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4919 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE OF THE MECHANOSENSITIVE CHANNEL MSCS EMBEDDED IN THE MEMBRANE BILAYER | |||||||||
Map data | RELION post-processed map; no mask; applied b-factor of -139; new box 250 px | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / monoatomic ion transmembrane transport / protein homooligomerization / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / Resolution: 2.9 Å | |||||||||
Authors | Rasmussen T / Flegler VJ / Rasmussen A / Boettcher B | |||||||||
Funding support | Germany, 2 items
| |||||||||
Citation | Journal: J Mol Biol / Year: 2019 Title: Structure of the Mechanosensitive Channel MscS Embedded in the Membrane Bilayer. Authors: Tim Rasmussen / Vanessa J Flegler / Akiko Rasmussen / Bettina Böttcher / Abstract: Since life has emerged, gradients of osmolytes over the cell membrane cause pressure changes in the cell and require tight regulation to prevent cell rupture. The mechanosensitive channel of small ...Since life has emerged, gradients of osmolytes over the cell membrane cause pressure changes in the cell and require tight regulation to prevent cell rupture. The mechanosensitive channel of small conductance (MscS) releases solutes and water when a hypo-osmotic shock raises the pressure in the cell. It is a member of a large family of MscS-like channels found in bacteria, archaea, fungi and plants and model for mechanosensation. MscS senses the increase of tension in the membrane directly by the force from the lipids, but the molecular mechanism is still elusive. We determined the lipid interactions of MscS by resolving the structure of Escherichia coli MscS embedded in membrane discs to 2.9-Å resolution using cryo-electron microscopy. The membrane is attached only to parts of the sensor paddles of MscS, but phospholipid molecules move through grooves into remote pockets on the cytosolic side. On the periplasmic side, a lipid bound by R88 at the pore entrance is separated from the membrane by TM1 helices. The N-terminus interacts with the periplasmic membrane surface. We demonstrate that the unique membrane domain of MscS promotes deep penetration of lipid molecules and shows multimodal interaction with the membrane to fine-tune tension sensing. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4919.map.gz | 55.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4919-v30.xml emd-4919.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4919_fsc.xml | 21.1 KB | Display | FSC data file |
Images | emd_4919.png | 52.2 KB | ||
Others | emd_4919_half_map_1.map.gz emd_4919_half_map_2.map.gz | 54 MB 54.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4919 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4919 | HTTPS FTP |
-Related structure data
Related structure data | 6rldMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4919.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | RELION post-processed map; no mask; applied b-factor of -139; new box 250 px | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0635 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: RELION unfiltered half map; last refinement; new box 250 px
File | emd_4919_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | RELION unfiltered half map; last refinement; new box 250 px | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: RELION unfiltered half map; last refinement; new box 250 px
File | emd_4919_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | RELION unfiltered half map; last refinement; new box 250 px | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : MSCS IN NANODISCS
Entire | Name: MSCS IN NANODISCSMicrosoft Cluster Server |
---|---|
Components |
|
-Supramolecule #1: MSCS IN NANODISCS
Supramolecule | Name: MSCS IN NANODISCS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: MSCS WITH MSP1E3D1 AND AZOLECTINE |
---|---|
Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
-Macromolecule #1: Small-conductance mechanosensitive channel
Macromolecule | Name: Small-conductance mechanosensitive channel / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 30.922898 KDa |
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 KRVKEDKAA |
-Macromolecule #2: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 21 / Formula: PCW |
---|---|
Molecular weight | Theoretical: 787.121 Da |
Chemical component information | ChemComp-PCW: |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
---|---|
Aggregation state | particle |
-Sample preparation
Concentration | 0.40 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Details: QUANTIFOIL R1.2/1.3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Number real images: 4160 / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON III (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Number real images: 1133 / #1 - Average electron dose: 56.0 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: FEI FALCON III (4k x 4k) / #2 - Detector mode: INTEGRATING / #2 - Number real images: 3086 / #2 - Average electron dose: 75.0 e/Å2 / #3 - Image recording ID: 4 / #3 - Film or detector model: FEI FALCON III (4k x 4k) / #3 - Detector mode: INTEGRATING / #3 - Number real images: 3738 / #3 - Average electron dose: 100.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |