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- PDB-6vyk: Cryo-EM structure of mechanosensitive channel MscS in PC-18:1 nan... -

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Basic information

Entry
Database: PDB / ID: 6vyk
TitleCryo-EM structure of mechanosensitive channel MscS in PC-18:1 nanodiscs
ComponentsMechanosensitive channel MscS
KeywordsMEMBRANE PROTEIN / Mechanosensitive channel / MscS / Nanodiscs / Lipid
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
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Small-conductance mechanosensitive channel / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang, Y. / Daday, C. / Gu, R. / Cox, C.D. / Martinac, B. / Groot, B. / Walz, T.
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Mechanosensitive channel MscS
B: Mechanosensitive channel MscS
C: Mechanosensitive channel MscS
D: Mechanosensitive channel MscS
E: Mechanosensitive channel MscS
F: Mechanosensitive channel MscS
G: Mechanosensitive channel MscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,97014
Polymers216,4607
Non-polymers5,5107
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Mechanosensitive channel MscS / Mechanosensitive channel protein / small conductance / Mechanosensitive ion channel protein MscS / ...Mechanosensitive channel protein / small conductance / Mechanosensitive ion channel protein MscS / MscS / Protein YggB / Protein involved in stability of MscS mechanosensitive channel / Small-conductance mechanosensitive channel / Small-conductance mechanosensitive channel MscS / Transport protein


Mass: 30922.898 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mscS, mscS_1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3SVH2, UniProt: P0C0S1*PLUS
#2: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C44H85NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPC, phospholipid*YM
Has ligand of interestY

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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: Mechanosensitive channel MscS / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.21 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98111 / Symmetry type: POINT

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