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- PDB-6vxm: Cryo-EM structure of Arabidopsis thaliana MSL1 -

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Basic information

Entry
Database: PDB / ID: 6vxm
TitleCryo-EM structure of Arabidopsis thaliana MSL1
ComponentsMechanosensitive ion channel protein 1, mitochondrial
KeywordsTRANSPORT PROTEIN / ion channel
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / chloroplast envelope / chloroplast / cellular response to oxidative stress / mitochondrial inner membrane / mitochondrion
Similarity search - Function
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
EICOSANE / Mechanosensitive ion channel protein 1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsDeng, Z. / Zhang, J. / Yuan, P.
CitationJournal: Nat Commun / Year: 2020
Title: Structural mechanism for gating of a eukaryotic mechanosensitive channel of small conductance.
Authors: Zengqin Deng / Grigory Maksaev / Angela M Schlegel / Jingying Zhang / Michael Rau / James A J Fitzpatrick / Elizabeth S Haswell / Peng Yuan /
Abstract: Mechanosensitive ion channels transduce physical force into electrochemical signaling that underlies an array of fundamental physiological processes, including hearing, touch, proprioception, ...Mechanosensitive ion channels transduce physical force into electrochemical signaling that underlies an array of fundamental physiological processes, including hearing, touch, proprioception, osmoregulation, and morphogenesis. The mechanosensitive channels of small conductance (MscS) constitute a remarkably diverse superfamily of channels critical for management of osmotic pressure. Here, we present cryo-electron microscopy structures of a MscS homolog from Arabidopsis thaliana, MSL1, presumably in both the closed and open states. The heptameric MSL1 channel contains an unusual bowl-shaped transmembrane region, which is reminiscent of the evolutionarily and architecturally unrelated mechanosensitive Piezo channels. Upon channel opening, the curved transmembrane domain of MSL1 flattens and expands. Our structures, in combination with functional analyses, delineate a structural mechanism by which mechanosensitive channels open under increased membrane tension. Further, the shared structural feature between unrelated channels suggests the possibility of a unified mechanical gating mechanism stemming from membrane deformation induced by a non-planar transmembrane domain.
History
DepositionFeb 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 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 ion channel protein 1, mitochondrial
B: Mechanosensitive ion channel protein 1, mitochondrial
C: Mechanosensitive ion channel protein 1, mitochondrial
D: Mechanosensitive ion channel protein 1, mitochondrial
E: Mechanosensitive ion channel protein 1, mitochondrial
F: Mechanosensitive ion channel protein 1, mitochondrial
G: Mechanosensitive ion channel protein 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,96928
Polymers326,0367
Non-polymers5,93321
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area42010 Å2
ΔGint-191 kcal/mol
Surface area95810 Å2

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Components

#1: Protein
Mechanosensitive ion channel protein 1, mitochondrial / Mechanosensitive channel of small conductance-like 1 / MscS-Like protein 1 / MSL1


Mass: 46576.535 Da / Num. of mol.: 7 / Fragment: UNP residues 80-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MSL1, At4g00290, A_IG005I10.9, F5I10.9 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q8VZL4
#2: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C20H42
Has ligand of interestN

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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: MSL1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: OTHER
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1162GATAN K2 SUMMIT (4k x 4k)
2162GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158172 / Symmetry type: POINT

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