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- EMDB-30017: AtMSL1 wild type -

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Basic information

Entry
Database: EMDB / ID: EMD-30017
TitleAtMSL1 wild type
Map dataEM map at 3.3 angstrom
Sample
  • Complex: Wild type of AtMSL1
    • Protein or peptide: Mechanosensitive ion channel protein 1, mitochondrial
KeywordsMechanosensitive / Ion channel / Plant / MEMBRANE PROTEIN
Function / homology
Function and homology information


chloroplast envelope / mechanosensitive monoatomic ion channel activity / 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: 3.3 Å
AuthorsSun L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870732 China
CitationJournal: Cell Rep / Year: 2020
Title: Structural Insights into a Plant Mechanosensitive Ion Channel MSL1.
Authors: Yawen Li / Yufei Hu / Jiawei Wang / Xin Liu / Wei Zhang / Linfeng Sun /
Abstract: The small conductance mechanosensitive ion channel (MscS)-like (MSL) proteins in plants are evolutionarily conserved homologs of the bacterial small conductance mechanosensitive ion channels. As the ...The small conductance mechanosensitive ion channel (MscS)-like (MSL) proteins in plants are evolutionarily conserved homologs of the bacterial small conductance mechanosensitive ion channels. As the sole member of the Arabidopsis MSL family localized in the mitochondrial inner membrane, MSL1 is essential to maintain the normal membrane potential of mitochondria. Here, we report a cryoelectron microscopy (cryo-EM) structure of Arabidopsis thaliana MSL1 (AtMSL1) at 3.3 Å. The overall architecture of AtMSL1 is similar to MscS. However, the transmembrane domain of AtMSL1 is larger. Structural differences are observed in both the transmembrane and the matrix domain of AtMSL1. The carboxyl-terminus of AtMSL1 is more flexible and the β-barrel structure observed in MscS is absent. The side portals in AtMSL1 are significantly smaller, and enlarging the size of the portal by mutagenesis can increase the channel conductance. Our study provides a framework for eukaryotic MscS-like mechanosensitive ion channels and the gating mechanism of the MscS family.
History
DepositionFeb 15, 2020-
Header (metadata) releaseApr 15, 2020-
Map releaseApr 15, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lyp
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30017.png

Downloads & links

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Map

FileDownload / File: emd_30017.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map at 3.3 angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.04
Minimum - Maximum-0.30197898 - 0.45447677
Average (Standard dev.)0.00017022021 (±0.011303584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
start NX/NY/NZ107107101
NX/NY/NZ267267267
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.3020.4540.000

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Supplemental data

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Half map: Half 1 map

Fileemd_30017_half_map_1.map
AnnotationHalf 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 2 map

Fileemd_30017_half_map_2.map
AnnotationHalf 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 : Wild type of AtMSL1

EntireName: Wild type of AtMSL1
Components
  • Complex: Wild type of AtMSL1
    • Protein or peptide: Mechanosensitive ion channel protein 1, mitochondrial

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Supramolecule #1: Wild type of AtMSL1

SupramoleculeName: Wild type of AtMSL1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 350 KDa

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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: 53.942 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGVRLSLLK SIQRSIKPHA TAKSCSGLLN SHARAFTCGN LLDGPKASPS MISFSSNIRL HNDAKPFNYL GHSSYARAFS SKSDDFGSI VASGVTGSGD GNGNGNDWVE KAKDVLQTSV DAVTETAKKT KDVSDEMIPH VQQFLDSNPY LKDVIVPVSL T MTGTLFAW ...String:
MAGVRLSLLK SIQRSIKPHA TAKSCSGLLN SHARAFTCGN LLDGPKASPS MISFSSNIRL HNDAKPFNYL GHSSYARAFS SKSDDFGSI VASGVTGSGD GNGNGNDWVE KAKDVLQTSV DAVTETAKKT KDVSDEMIPH VQQFLDSNPY LKDVIVPVSL T MTGTLFAW VVMPRILRRF HTYAMQSSAK LLPVGFSNED VPYEKSFWGA LEDPARYLVT FIAFAQIAAM VAPTTAIAQY FS PTVKGAV ILSLVWFLYR WKTNVITRML SAKSFGGLDR EKVLTLDKVS SVGLFAIGLM ASAEACGVAV QSILTVGGVG GVA TAFAAR DILGNVLSGL SMQFSRPFSM GDTIKAGSVE GQVIEMGLTT TSLLNAEKFP VLVPNSLFSS QVIVNKSRAQ WRAI ASKIP LQIDDLDMIP QISNEIKEML RSNTKVFLGK EAPHCYLSRV EKSFAELTIG CNLIRMGKEE LYNTQQEVLL EAVKI IKKH GVSLGTTWDN STL

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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 251528
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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