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- EMDB-41168: Cryo-EM structure of AtMSL10-K539E -

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Basic information

Entry
Database: EMDB / ID: EMD-41168
TitleCryo-EM structure of AtMSL10-K539E
Map dataNU-refinement
Sample
  • Complex: AtMSL10 with mutation K539E
    • Protein or peptide: Mechanosensitive ion channel protein 10Mechanosensitive channels
Keywordsion channels / mechanosensitive channels / heptamer / Arabidopsis thaliana / TRANSPORT PROTEIN
Function / homology
Function and homology information


programmed cell death in response to reactive oxygen species / leaf senescence / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / monoatomic anion transport / plasma membrane
Similarity search - Function
Mechanosensitive ion channel MscS-like, plants/fungi / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / LSM domain superfamily
Similarity search - Domain/homology
Mechanosensitive ion channel protein 10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang J / Yuan P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM143440 United States
CitationJournal: Nat Commun / Year: 2023
Title: Open structure and gating of the Arabidopsis mechanosensitive ion channel MSL10.
Authors: Jingying Zhang / Grigory Maksaev / Peng Yuan /
Abstract: Plants are challenged by drastically different osmotic environments during growth and development. Adaptation to these environments often involves mechanosensitive ion channels that can detect and ...Plants are challenged by drastically different osmotic environments during growth and development. Adaptation to these environments often involves mechanosensitive ion channels that can detect and respond to mechanical force. In the model plant Arabidopsis thaliana, the mechanosensitive channel MSL10 plays a crucial role in hypo-osmotic shock adaptation and programmed cell death induction, but the molecular basis of channel function remains poorly understood. Here, we report a structural and electrophysiological analysis of MSL10. The cryo-electron microscopy structures reveal a distinct heptameric channel assembly. Structures of the wild-type channel in detergent and lipid environments, and in the absence of membrane tension, capture an open conformation. Furthermore, structural analysis of a non-conductive mutant channel demonstrates that reorientation of phenylalanine side chains alone, without main chain rearrangements, may generate the hydrophobic gate. Together, these results reveal a distinct gating mechanism and advance our understanding of mechanotransduction.
History
DepositionJul 3, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41168.png

Downloads & links

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Map

FileDownload / File: emd_41168.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNU-refinement
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.7824686 - 1.8973415
Average (Standard dev.)-0.0005066853 (±0.07598087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepEMhancer

Fileemd_41168_additional_1.map
AnnotationdeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_41168_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_41168_half_map_1.map
Annotationhalf_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_41168_half_map_2.map
Annotationhalf_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AtMSL10 with mutation K539E

EntireName: AtMSL10 with mutation K539E
Components
  • Complex: AtMSL10 with mutation K539E
    • Protein or peptide: Mechanosensitive ion channel protein 10Mechanosensitive channels

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Supramolecule #1: AtMSL10 with mutation K539E

SupramoleculeName: AtMSL10 with mutation K539E / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Mechanosensitive ion channel protein 10

MacromoleculeName: Mechanosensitive ion channel protein 10 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 83.9555 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MAEQKSSNGG GGGGDVVINV PVEEASRRSK EMASPESEKG VPFSKSPSPE ISKLVGSPNK PPRAPNQNNV GLTQRKSFAR SVYSKPKSR FVDPSCPVDT SILEEEVREQ LGAGFSFSRA SPNNKSNRSV GSPAPVTPSK VVVEKDEDEE IYKKVKLNRE M RSKISTLA ...String:
MAEQKSSNGG GGGGDVVINV PVEEASRRSK EMASPESEKG VPFSKSPSPE ISKLVGSPNK PPRAPNQNNV GLTQRKSFAR SVYSKPKSR FVDPSCPVDT SILEEEVREQ LGAGFSFSRA SPNNKSNRSV GSPAPVTPSK VVVEKDEDEE IYKKVKLNRE M RSKISTLA LIESAFFVVI LSALVASLTI NVLKHHTFWG LEVWKWCVLV MVIFSGMLVT NWFMRLIVFL IETNFLLRRK VL YFVHGLK KSVQVFIWLC LILVAWILLF NHDVKRSPAA TKVLKCITRT LISILTGAFF WLVKTLLLKI LAANFNVNNF FDR IQDSVF HQYVLQTLSG LPLMEEAERV GREPSTGHLS FATVVKKGTV KEKKVIDMGK VHKMKREKVS AWTMRVLMEA VRTS GLSTI SDTLDETAYG EGKEQADREI TSEMEALAAA YHVFRNVAQP FFNYIEEEDL LRFMIKEEVD LVFPLFDGAA ETGRI TRKA FTEWVVKVYT SRRALAHSLN DTKTAVKQLN KLVTAILMVV TVVIWLLLLE VATTEVLLFF STQLVALAFI IGSTCK NLF ESIVFVFVMH PYDVGDRCVV DGVAMLVEEM NLLTTVFLKL NNEKVYYPNA VLATKPISNY FRSPNMGETV EFSISFS TP VSKIAHLKER IAEYLEQNPQ HWAPVHSVVV KEIENMNKLK MALYSDHTIT FQENRERNLR RTELSLAIKR MLEDLHID Y TLLPQDINLT KKNSLEVLFQ

UniProtKB: Mechanosensitive ion channel protein 10

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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: 8
Component:
ConcentrationFormulaName
150.0 mmol/LNaClSodium chloridesodium chloride
20.0 mmol/LTris hydrochloride
0.04 mmol/Lglyco-diosgenin

Details: 20 mM Tris-HCl PH 8.0, 150 mM NaCl, and 0.04 mM GDN
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsAtMSL10-K539E in detergent

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 3229 / Average electron dose: 44.0 e/Å2

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Image processing

Particle selectionNumber selected: 1017121
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8tdj

Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 326262

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Atomic model buiding 1

Initial modelPDB ID:

8tdj


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8tdm:
Cryo-EM structure of AtMSL10-K539E

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