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- EMDB-21447: Cryo-EM structure of Arabidopsis thaliana MSL1 in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-21447
TitleCryo-EM structure of Arabidopsis thaliana MSL1 in lipid nanodisc
Map dataArabidopsis thaliana MSL1 in lipid nanodisc
Sample
  • Complex: MSL1
    • Protein or peptide: Mechanosensitive ion channel protein 1, mitochondrial
Keywordsion channel / TRANSPORT PROTEIN
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
Mechanosensitive ion channel protein 1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 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, 2020-
Header (metadata) releaseMar 4, 2020-
Map releaseAug 5, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vxp
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vxp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21447.png

Downloads & links

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Map

FileDownload / File: emd_21447.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationArabidopsis thaliana MSL1 in lipid nanodisc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.014
Minimum - Maximum-0.016663957 - 0.06078327
Average (Standard dev.)0.00030147407 (±0.0022522432)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-2141-44
NX/NY/NZ1079792
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0170.0610.000

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Supplemental data

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Sample components

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Entire : MSL1

EntireName: MSL1
Components
  • Complex: MSL1
    • Protein or peptide: Mechanosensitive ion channel protein 1, mitochondrial

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Supramolecule #1: MSL1

SupramoleculeName: MSL1 / 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 1, mitochondrial

MacromoleculeName: Mechanosensitive ion channel protein 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 46.576535 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MSSKSDDFGS IVASGVTGSG DGNGNGNDWV EKAKDVLQTS VDAVTETAKK TKDVSDEMIP HVQQFLDSNP YLKDVIVPVS LTMTGTLFA WVVMPRILRR FHTYAMQSSA KLLPVGFSNE DVPYEKSFWG ALEDPARYLV TFIAFAQIAA MVAPTTIAAQ Y FSPTVKGA ...String:
MSSKSDDFGS IVASGVTGSG DGNGNGNDWV EKAKDVLQTS VDAVTETAKK TKDVSDEMIP HVQQFLDSNP YLKDVIVPVS LTMTGTLFA WVVMPRILRR FHTYAMQSSA KLLPVGFSNE DVPYEKSFWG ALEDPARYLV TFIAFAQIAA MVAPTTIAAQ Y FSPTVKGA VILSLVWFLY RWKTNVITRM LSAKSFGGLD REKVLTLDKV SSVGLFAIGL MASAEACGVA VQSILTVGGV GG VATAFAA RDILGNVLSG LSMQFSRPFS MGDTIKAGSV EGQVIEMGLT TTSLLNAEKF PVLVPNSLFS SQVIVNKSRA QWR AIASKI PLQIDDLDMI PQISNEIKEM LRSNTKVFLG KEAPHCYLSR VEKSFAELTI GCNLIRMGKE ELYNTQQEVL LEAV KIIKK HGVSLGTTWD NSTLSNSLEV LFQ

UniProtKB: Mechanosensitive ion channel protein 1, mitochondrial

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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

Concentration1 mg/mL
BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 62.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23077
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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