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- EMDB-21462: Cryo-EM structure of mechanosensitive channel MscS in PC-18:1 nan... -

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Basic information

Entry
Database: EMDB / ID: EMD-21462
TitleCryo-EM structure of mechanosensitive channel MscS in PC-18:1 nanodiscs
Map datastructure of mechanosensitive channel MscS in PC-18:1 nanodiscs
Sample
  • Complex: Mechanosensitive channel MscS
    • Protein or peptide: Mechanosensitive channel MscS
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsMechanosensitive channel / MscS / Nanodiscs / Lipid / MEMBRANE PROTEIN
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / protein homooligomerization / monoatomic ion transmembrane transport / identical protein binding / membrane / 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 / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang Y / Daday C
CitationJournal: Nature / Year: 2021
Title: Visualization of the mechanosensitive ion channel MscS under membrane tension.
Authors: Yixiao Zhang / Csaba Daday / Ruo-Xu Gu / Charles D Cox / Boris Martinac / Bert L de Groot / Thomas Walz /
Abstract: Mechanosensitive channels sense mechanical forces in cell membranes and underlie many biological sensing processes. However, how exactly they sense mechanical force remains under investigation. The ...Mechanosensitive channels sense mechanical forces in cell membranes and underlie many biological sensing processes. However, how exactly they sense mechanical force remains under investigation. The bacterial mechanosensitive channel of small conductance, MscS, is one of the most extensively studied mechanosensitive channels, but how it is regulated by membrane tension remains unclear, even though the structures are known for its open and closed states. Here we used cryo-electron microscopy to determine the structure of MscS in different membrane environments, including one that mimics a membrane under tension. We present the structures of MscS in the subconducting and desensitized states, and demonstrate that the conformation of MscS in a lipid bilayer in the open state is dynamic. Several associated lipids have distinct roles in MscS mechanosensation. Pore lipids are necessary to prevent ion conduction in the closed state. Gatekeeper lipids stabilize the closed conformation and dissociate with membrane tension, allowing the channel to open. Pocket lipids in a solvent-exposed pocket between subunits are pulled out under sustained tension, allowing the channel to transition to the subconducting state and then to the desensitized state. Our results provide a mechanistic underpinning and expand on the 'force-from-lipids' model for MscS mechanosensation.
History
DepositionFeb 27, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseFeb 10, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / 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-6vyk
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21462.png

Downloads & links

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Map

FileDownload / File: emd_21462.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of mechanosensitive channel MscS in PC-18:1 nanodiscs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 216 pix.
= 216. Å		1 Å/pix.
x 216 pix.
= 216. Å		1 Å/pix.
x 216 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.23390034 - 0.40066573
Average (Standard dev.)0.0002386471 (±0.013094086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.2340.4010.000

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Supplemental data

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Sample components

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Entire : Mechanosensitive channel MscS

EntireName: Mechanosensitive channel MscS
Components
  • Complex: Mechanosensitive channel MscS
    • Protein or peptide: Mechanosensitive channel MscS
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Mechanosensitive channel MscS

SupramoleculeName: Mechanosensitive channel MscS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: Mechanosensitive channel MscS

MacromoleculeName: Mechanosensitive channel MscS / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.922898 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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

UniProtKB: Small-conductance mechanosensitive channel

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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: 7 / 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98111
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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