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- PDB-8tdl: Cryo-EM structure of the wild-type AtMSL10 in saposin -

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Basic information

Entry
Database: PDB / ID: 8tdl
TitleCryo-EM structure of the wild-type AtMSL10 in saposin
ComponentsMechanosensitive ion channel protein 10
KeywordsTRANSPORT PROTEIN / ion channels / mechanosensitive channels / heptamer / Arabidopsis thaliana
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhang, J. / Yuan, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM143440 United States
CitationJournal: Nat Commun / Year: 2023
Title: Open structure and gating of the Arabidopsis mechanosensitive ion channel MSL10.
Authors: Jingying Zhang / Grigory Maksaev / Peng Yuan /
Abstract: Plants are challenged by drastically different osmotic environments during growth and development. Adaptation to these environments often involves mechanosensitive ion channels that can detect and ...Plants are challenged by drastically different osmotic environments during growth and development. Adaptation to these environments often involves mechanosensitive ion channels that can detect and respond to mechanical force. In the model plant Arabidopsis thaliana, the mechanosensitive channel MSL10 plays a crucial role in hypo-osmotic shock adaptation and programmed cell death induction, but the molecular basis of channel function remains poorly understood. Here, we report a structural and electrophysiological analysis of MSL10. The cryo-electron microscopy structures reveal a distinct heptameric channel assembly. Structures of the wild-type channel in detergent and lipid environments, and in the absence of membrane tension, capture an open conformation. Furthermore, structural analysis of a non-conductive mutant channel demonstrates that reorientation of phenylalanine side chains alone, without main chain rearrangements, may generate the hydrophobic gate. Together, these results reveal a distinct gating mechanism and advance our understanding of mechanotransduction.
History
DepositionJul 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mechanosensitive ion channel protein 10
B: Mechanosensitive ion channel protein 10
C: Mechanosensitive ion channel protein 10
D: Mechanosensitive ion channel protein 10
E: Mechanosensitive ion channel protein 10
F: Mechanosensitive ion channel protein 10
G: Mechanosensitive ion channel protein 10


Theoretical massNumber of molelcules
Total (without water)587,6897
Polymers587,6897
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "G"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "C"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 166 - 731 / Label seq-ID: 166 - 731

Dom-IDAuth asym-IDLabel asym-ID
d_1GG
d_2BB
d_3AA
d_4DD
d_5EE
d_6FF
d_7CC

NCS oper:
IDCodeMatrixVector
1given(-0.222519210934, 0.974928305449, -4.40413498351E-7), (-0.974928305449, -0.222519210934, -1.79859011179E-7), (-2.73350105126E-7, 3.89349500397E-7, 1)40.8525970105, 362.578894703, -1.30482971201E-5
2given(0.623489934272, 0.781831376872, 7.9832603551E-8), (-0.781831376872, 0.623489934272, -1.59346609724E-7), (-1.74357004021E-7, 3.69353728699E-8, 1)-66.8780232361, 191.126357764, 2.08450341574E-5
3given(-0.900969329797, -0.433882779982, 1.69727292221E-7), (0.433882779982, -0.900969329797, -1.04607410251E-7), (1.98306438688E-7, -2.0606318918E-8, 1)385.250609267, 242.069262981, -2.7554758077E-5
4given(-0.222521729872, -0.974927730519, 4.43046596807E-7), (0.974927730519, -0.222521729872, -1.31037761278E-8), (1.11362729857E-7, 4.29022538207E-7, 1)362.579078657, 40.8529906239, -7.52724133122E-5
5given(0.623489276599, -0.781831901348, -8.98783693875E-8), (0.781831901348, 0.623489276599, -2.43493795929E-7), (2.46409416949E-7, 8.15459942517E-8, 1)191.12652767, -66.8779543569, -4.87282646588E-5
6given(-0.900968503123, 0.433884496589, -2.16936498996E-7), (-0.43388449659, -0.900968503123, 1.18102097513E-7), (-1.44210283647E-7, 2.0053165367E-7, 1)242.06892164, 385.250719604, -6.60111263073E-6

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Components

#1: Protein
Mechanosensitive ion channel protein 10


Mass: 83955.562 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MSL10 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9LYG9

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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: AtMSL10 in saposin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl and 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mmol/Lsodium chlorideNaCl1
220 mmol/LTris hydrochloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 0.01 mm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 2120

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
7Coot0.9model fitting
11RELION3classification
12cryoSPARC3D reconstruction
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 404639
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69275 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 8TDJ

8tdj


Accession code: 8TDJ / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 159.35 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002817808
ELECTRON MICROSCOPYf_angle_d0.481524381
ELECTRON MICROSCOPYf_chiral_restr0.03893080
ELECTRON MICROSCOPYf_plane_restr0.00373129
ELECTRON MICROSCOPYf_dihedral_angle_d3.76072632
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2GGELECTRON MICROSCOPYNCS constraints0.000578519227278
ens_1d_3GGELECTRON MICROSCOPYNCS constraints0.00057795954281
ens_1d_4GGELECTRON MICROSCOPYNCS constraints0.000579106863333
ens_1d_5GGELECTRON MICROSCOPYNCS constraints0.000582844667217
ens_1d_6GGELECTRON MICROSCOPYNCS constraints0.000581285280956
ens_1d_7GGELECTRON MICROSCOPYNCS constraints0.000575775266812

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