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- PDB-6lyp: Cryo-EM structure of AtMSL1 wild type -

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Basic information

Entry
Database: PDB / ID: 6lyp
TitleCryo-EM structure of AtMSL1 wild type
ComponentsMechanosensitive ion channel protein 1, mitochondrialMechanosensitive channels
KeywordsMEMBRANE PROTEIN / Mechanosensitive / Ion channel / Plant
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSun, L.
Funding support China, 1items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Mechanosensitive ion channel protein 1, mitochondrial
B: Mechanosensitive ion channel protein 1, mitochondrial
C: Mechanosensitive ion channel protein 1, mitochondrial
D: Mechanosensitive ion channel protein 1, mitochondrial
E: Mechanosensitive ion channel protein 1, mitochondrial
F: Mechanosensitive ion channel protein 1, mitochondrial
G: Mechanosensitive ion channel protein 1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)377,5947
Polymers377,5947
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area34160 Å2
ΔGint-240 kcal/mol
Surface area90490 Å2

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Components

#1: Protein
Mechanosensitive ion channel protein 1, mitochondrial / Mechanosensitive channels / Mechanosensitive channel of small conductance-like 1 / MscS-Like protein 1


Mass: 53942.000 Da / Num. of mol.: 7 / Mutation: I234A, A235I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MSL1, At4g00290, A_IG005I10.9, F5I10.9 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q8VZL4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Wild type of AtMSL1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.35 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
12RELION3.13D reconstruction
13PHENIX1.17.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251528 / Symmetry type: POINT
RefinementCross valid method: NONE

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