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- EMDB-41164: Cryo-EM structure of the wild-type AtMSL10 in GDN -

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Basic information

Entry
Database: EMDB / ID: EMD-41164
TitleCryo-EM structure of the wild-type AtMSL10 in GDN
Map dataNU-refinement
Sample
  • Complex: Homo-heptameric AtMSL10 channel
    • Protein or peptide: Mechanosensitive ion channel protein 10
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_41164.png

Downloads & links

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Map

FileDownload / File: emd_41164.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNU-refinement
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-0.58932245 - 1.7567968
Average (Standard dev.)0.00009166805 (±0.06661737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepEMhancer

Fileemd_41164_additional_1.map
AnnotationdeepEMhancer
Projections & Slices
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Additional map: #1

Fileemd_41164_additional_2.map
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Half map: half B

Fileemd_41164_half_map_1.map
Annotationhalf_B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half A

Fileemd_41164_half_map_2.map
Annotationhalf_A
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Sample components

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Entire : Homo-heptameric AtMSL10 channel

EntireName: Homo-heptameric AtMSL10 channel
Components
  • Complex: Homo-heptameric AtMSL10 channel
    • Protein or peptide: Mechanosensitive ion channel protein 10

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Supramolecule #1: Homo-heptameric AtMSL10 channel

SupramoleculeName: Homo-heptameric AtMSL10 channel / 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: 83.955562 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 VATTKVLLFF 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 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 in detergent

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 3828 / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000

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Image processing

Particle selectionNumber selected: 648864
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold AtMSL10
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: 163661
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial modelPDB ID:

lyg9


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8tdj:
Cryo-EM structure of the wild-type AtMSL10 in GDN

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