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- EMDB-78957: Cryo-EM structure of wild-type Arabidopsis thaliana mechanosensit... -

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Basic information

Entry
Database: EMDB / ID: EMD-78957
TitleCryo-EM structure of wild-type Arabidopsis thaliana mechanosensitive channel of small conductance-like protein 2 (MSL2) in DOPC lipid nanodiscs.
Map dataUnsharpened cryo-EM map for WT-MSL2 in DOPC
Sample
  • Complex: Mechanosensitive channel protein 2 (MSL2) from Arabidopsis thaliana
    • Protein or peptide: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein
KeywordsMechanosensitive channel / membrane protein / nanodiscs
Function / homology
Function and homology information


plastid envelope / chloroplast fission / chloroplast membrane / cellular response to osmotic stress / monoatomic ion channel activity / bioluminescence / generation of precursor metabolites and energy / chloroplast / plasma membrane
Similarity search - Function
: / : / Mechanosensitive ion channel protein 2/3 C-terminal / Mechanosensitive channel protein 2/3 domain / Mechanosensitive ion channel protein YnaI-like / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / LSM domain superfamily / Green fluorescent protein, GFP ...: / : / Mechanosensitive ion channel protein 2/3 C-terminal / Mechanosensitive channel protein 2/3 domain / Mechanosensitive ion channel protein YnaI-like / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / LSM domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Mechanosensitive ion channel protein 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsAngiulli G / Dong L / Walz T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM144581 United States
CitationJournal: To Be Published
Title: The MscS-like mechanosensitive channel MSL2 from plant chloroplasts is constitutively open
Authors: Dong L / Angiulli G / Cheng D / Nakayama Y / Hiotis G / Cox CD / Walz T
History
DepositionSep 8, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78957.png

Downloads & links

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Map

FileDownload / File: emd_78957.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened cryo-EM map for WT-MSL2 in DOPC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.147
Minimum - Maximum-0.26422292 - 1.0751859
Average (Standard dev.)0.002135957 (±0.035562504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Unsharpened cryo-EM half map B for WT-MSL2 in DOPC

Fileemd_78957_half_map_1.map
AnnotationUnsharpened cryo-EM half map B for WT-MSL2 in DOPC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened cryo-EM half map A for WT-MSL2 in DOPC

Fileemd_78957_half_map_2.map
AnnotationUnsharpened cryo-EM half map A for WT-MSL2 in DOPC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mechanosensitive channel protein 2 (MSL2) from Arabidopsis thaliana

EntireName: Mechanosensitive channel protein 2 (MSL2) from Arabidopsis thaliana
Components
  • Complex: Mechanosensitive channel protein 2 (MSL2) from Arabidopsis thaliana
    • Protein or peptide: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein

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Supramolecule #1: Mechanosensitive channel protein 2 (MSL2) from Arabidopsis thaliana

SupramoleculeName: Mechanosensitive channel protein 2 (MSL2) from Arabidopsis thaliana
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 670 KDa

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Macromolecule #1: Mechanosensitive ion channel protein 2, chloroplastic,Green fluor...

MacromoleculeName: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 95.841203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MCHSFSASGK AIEPAVKAVT VVLTKSHGLM QQFPFVYKLV PAVALLVFSL WGLVPFARQG RNILLNKNDN GWKKSGTYHV MTSYVQPLL LWLGALFICR ALDPVVLPTE ASKIVKDRLL NFVRSLSTVL AFAYCLSSLI QQTQKLFSET SNPSDTRNMG F QFAGKALY ...String:
MCHSFSASGK AIEPAVKAVT VVLTKSHGLM QQFPFVYKLV PAVALLVFSL WGLVPFARQG RNILLNKNDN GWKKSGTYHV MTSYVQPLL LWLGALFICR ALDPVVLPTE ASKIVKDRLL NFVRSLSTVL AFAYCLSSLI QQTQKLFSET SNPSDTRNMG F QFAGKALY SAVWVAAVSL FMELLGFSTQ KWLTAGGLGT VLITLAGREI LTNFLSSVMI HATRPFVLNE WIQTKIEGYE VS GTVEHVG WWSPTIIRGE DREAIHIPNH KFTVNVVRNL TQKTHWRIKT HLAISHLDVN KINNIVADMR KVLAKNPMVE QQR LHRRVF LENVIPENQA LSILISCFVK TSHHEEYLGV KEAILLDLLR VISHHRARLA TPIRTIRKMY TETDVENTPF GESM YGGVT SRRPLMLIEP AYKINGEDKS KSQNRAAKPT AEQENKGSNP KSKETSSPDL KANVKVGESP VSDTNKVPEE TVAKP VIKA VSKPPTPKDT ETSGTEKPKA KRSGGTIKST KTDETDSSTS SASRSTLEEN IVLGVALEGS KRTLPIEEEI HSPPME TDA KELTGARRSG GNGPLVADKE QKDSQSQPNS GASTEPSNSL EVLFQGPTAA AAVSKGEELF TGVVPILVEL DGDVNGH KF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGN Y KTRAEVKFEG DTLVNRIELK GIDFKEDGNI LGHKLEYNYN SHNVYIMADK QKNGIKVNFK IRHNIEDGSV QLADHYQQN TPIGDGPVLL PDNHYLSTQS KLSKDPNEKR DHMVLLEFVT AAGITLGMDE LYKSGGGTET SQVAPA

UniProtKB: Mechanosensitive ion channel protein 2, chloroplastic, Green fluorescent protein

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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

Concentration0.15 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
30.0 mMTris-HClTris hydrochloride
2.0 mMDTTdithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 20 s wait time, 1 s blotting time and -2 blot force..
DetailsThe protein concentration of samples was ~0.15 mg/ml and fluorinated octyl maltoside was added to a final concentration of 0.3 mM

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6804 / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 937269
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 937269
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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