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- PDB-38rk: Cryo-EM structure of the L274A mutant of the Arabidopsis thaliana... -

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Basic information

Entry
Database: PDB / ID: 38rk
TitleCryo-EM structure of the L274A mutant of the Arabidopsis thaliana mechanosensitive channel of small conductance-like protein 2 (MSL2) in DOPC lipid nanodiscs.
ComponentsMechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein
KeywordsMEMBRANE PROTEIN / Mechanosensitive channel / DOPC 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsAngiulli, G. / Dong, L. / Walz, T.
Funding support United States, 1items
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, C.D. / Walz, T.
History
DepositionSep 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein
B: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein
C: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein
D: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein
E: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein
F: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein
G: Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)670,5947
Polymers670,5947
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Mechanosensitive ion channel protein 2, chloroplastic,Green fluorescent protein / Mechanosensitive channel of small conductance-like 2 / MscS-Like protein 2


Mass: 95799.125 Da / Num. of mol.: 7 / Mutation: L274A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MSL2, At5g10490, F12B17.160, GFP / Cell line (production host): HEK293SGnTI- / Production host: Homo sapiens (human) / References: UniProt: Q56X46, UniProt: P42212
Has protein modificationN

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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: Mechanosensitive channel protein 2 (MSL2) from Arabidopsis thaliana
Type: COMPLEX / Details: The Leu274 was mutated to Ala residue. / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.67 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S GnTI-
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
230 mMtris hydrochlorideTris-HCl1
32 mMdithiothreitolDTT1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The protein concentration of the sample was ~0.15mg/ml and fluorinated octyl maltoside was added to a final concentration of 0.3mM.
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 20s wait time, 1s blotting time and -2 blotting force

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv3particle selection
2PHENIX1.20.1_4487model refinement
3SerialEMimage acquisition
5cryoSPARCv3CTF correction
10cryoSPARCv3initial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCv3classification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81059 / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311235
ELECTRON MICROSCOPYf_angle_d0.42715239
ELECTRON MICROSCOPYf_dihedral_angle_d3.8091477
ELECTRON MICROSCOPYf_chiral_restr0.0451799
ELECTRON MICROSCOPYf_plane_restr0.0031897

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