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- EMDB-4919: STRUCTURE OF THE MECHANOSENSITIVE CHANNEL MSCS EMBEDDED IN THE ME... -

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Basic information

Entry
Database: EMDB / ID: EMD-4919
TitleSTRUCTURE OF THE MECHANOSENSITIVE CHANNEL MSCS EMBEDDED IN THE MEMBRANE BILAYER
Map dataRELION post-processed map; no mask; applied b-factor of -139; new box 250 px
Sample
  • Complex: MSCS IN NANODISCSMicrosoft Cluster Server
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
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
Mechanosensitive ion channel MscS, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / 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, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / 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
Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / Resolution: 2.9 Å
AuthorsRasmussen T / Flegler VJ / Rasmussen A / Boettcher B
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research FoundationBo1150/15-1 Germany
German Research FoundationINST 93/903-1 FUGG Germany
CitationJournal: 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
DepositionMay 2, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseJul 24, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rld
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4919.png

Downloads & links

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Map

FileDownload / File: emd_4919.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION post-processed map; no mask; applied b-factor of -139; new box 250 px
Voxel sizeX=Y=Z: 1.0635 Å
Density
Contour LevelBy AUTHOR: 0.0259 / Movie #1: 0.03
Minimum - Maximum-0.10170747 - 0.24689966
Average (Standard dev.)-0.0000633177 (±0.008011345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 265.875 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06351.06351.0635
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z265.875265.875265.875
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.1020.247-0.000

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Supplemental data

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Half map: RELION unfiltered half map; last refinement; new box 250 px

Fileemd_4919_half_map_1.map
AnnotationRELION unfiltered half map; last refinement; new box 250 px
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: RELION unfiltered half map; last refinement; new box 250 px

Fileemd_4919_half_map_2.map
AnnotationRELION unfiltered half map; last refinement; new box 250 px
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MSCS IN NANODISCS

EntireName: MSCS IN NANODISCSMicrosoft Cluster Server
Components
  • Complex: MSCS IN NANODISCSMicrosoft Cluster Server
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: MSCS IN NANODISCS

SupramoleculeName: 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)

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Macromolecule #1: Small-conductance mechanosensitive channel

MacromoleculeName: 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 weightTheoretical: 30.922898 KDa
SequenceString: 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

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Macromolecule #2: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 21 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.40 mg/mL
BufferpH: 7.5
GridDetails: QUANTIFOIL R1.2/1.3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen 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

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER / Details: EMDB: 3035
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 302157
Image recording ID1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2oau

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6rld:
STRUCTURE OF THE MECHANOSENSITIVE CHANNEL MSCS EMBEDDED IN THE MEMBRANE BILAYER

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