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- EMDB-36680: The open structure of the mechanosensitive channel MSL10 in Arabi... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36680
TitleThe open structure of the mechanosensitive channel MSL10 in Arabidopsis thaliana
Map data
Sample
  • Complex: Heptameric MSL10
    • Protein or peptide: Mechanosensitive ion channel protein 10
KeywordsMechanosensitive channel / MEMBRANE 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: 2.74 Å
AuthorsSun L / Liu X / Li X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900885 China
CitationJournal: To be published
Title: Structural insights into a Plant Mechanosensitive Ion Channel AtMSL10
Authors: Sun L / Liu X / Li X
History
DepositionJun 28, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36680.png

Downloads & links

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Map

FileDownload / File: emd_36680.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 300 pix.
= 303. Å		1.01 Å/pix.
x 300 pix.
= 303. Å		1.01 Å/pix.
x 300 pix.
= 303. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.853532 - 6.0006065
Average (Standard dev.)0.0008900164 (±0.15430464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 303.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36680_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36680_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heptameric MSL10

EntireName: Heptameric MSL10
Components
  • Complex: Heptameric MSL10
    • Protein or peptide: Mechanosensitive ion channel protein 10

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Supramolecule #1: Heptameric MSL10

SupramoleculeName: Heptameric MSL10 / 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: 83.138625 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 KKN

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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 22500
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6lyp

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111376
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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