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- PDB-9h2p: YnaI in its open conformation purified in DDM showing ligand-fill... -

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Basic information

Entry
Database: PDB / ID: 9h2p
TitleYnaI in its open conformation purified in DDM showing ligand-filled pockets
ComponentsLow conductance mechanosensitive channel YnaI
KeywordsMEMBRANE PROTEIN / YnaI / mechanosensitive ion channel of E. coli / MscS-like
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / cellular response to osmotic stress / identical protein binding / plasma membrane
Similarity search - Function
Mechanosensitive ion channel protein YnaI-like / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS ...Mechanosensitive ion channel protein YnaI-like / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / 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
DODECANE / Low conductance mechanosensitive channel YnaI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsFlegler, V.J. / Bottcher, B. / Rasmussen, T. / Rasmussen, A. / Hedrich, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)343886090 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Mechanosensitive channel engineering: A study on the mixing and matching of YnaI and MscS sensor paddles and pores.
Authors: Vanessa J Flegler / Akiko Rasmussen / Rainer Hedrich / Tim Rasmussen / Bettina Böttcher /
Abstract: Osmotically varying environments are challenging for bacterial cells. Sudden drops in osmolytes cause an increased membrane tension and rupture the cells in the absence of protective mechanisms. One ...Osmotically varying environments are challenging for bacterial cells. Sudden drops in osmolytes cause an increased membrane tension and rupture the cells in the absence of protective mechanisms. One family of protective proteins are mechanosensitive channels of small conductance that open in response to membrane tension. Although these channels have a common architecture, they vary widely in the number of transmembrane helices, conductivity, and gating characteristics. Although there are various structures of channels in the open and closed state, the underlying common principles of the gating mechanism remain poorly understood. Here we show that YnaI opens by radial relocation of the transmembrane sensor paddles together with a shortening of the pore, which contrasts the prototypic smaller MscS. A chimera of both channels with the YnaI sensor paddles and the pore containing C-terminal part of MscS is functional and has the tension response of the paddle donor. Our research shows that elements with different structural opening mechanisms can be mixed and matched within one channel as long as they support the common area expansion on the periplasmic side.
History
DepositionOct 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low conductance mechanosensitive channel YnaI
B: Low conductance mechanosensitive channel YnaI
C: Low conductance mechanosensitive channel YnaI
D: Low conductance mechanosensitive channel YnaI
E: Low conductance mechanosensitive channel YnaI
F: Low conductance mechanosensitive channel YnaI
G: Low conductance mechanosensitive channel YnaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,33049
Polymers262,1767
Non-polymers7,15442
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
Low conductance mechanosensitive channel YnaI


Mass: 37453.730 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ynaI, b1330, JW1323 / Production host: Escherichia coli (E. coli) / Strain (production host): MJF641 / References: UniProt: P0AEB5
#2: Chemical...
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: E. coli YnaI in its open conformation / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: MJF641 / Plasmid: pTrc
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
250 mMHEPESC8H18N2O4S1
30.03 %DDMC24H46O111
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 4 s blotting, blot force +25

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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: 75000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.39 sec. / Electron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of real images: 9866
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 5 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
4cryoSPARC4.3CTF correction
10cryoSPARC4.3initial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC4.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2829312
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180381 / Symmetry type: POINT
Atomic model buildingB value: 37 / Protocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00219334
ELECTRON MICROSCOPYf_angle_d0.3225984
ELECTRON MICROSCOPYf_dihedral_angle_d3.7972898
ELECTRON MICROSCOPYf_chiral_restr0.0372982
ELECTRON MICROSCOPYf_plane_restr0.0023171

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