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- EMDB-51817: a YnaI-MscS chimera in a closed conformation purified in DDM with... -

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Basic information

Entry
Database: EMDB / ID: EMD-51817
Titlea YnaI-MscS chimera in a closed conformation purified in DDM with additional lipids showing ligand-filled pore and pockets
Map data
Sample
  • Complex: A YnaI-MscS chimera in a closed conformation
    • Protein or peptide: Low conductance mechanosensitive channel YnaI,Small-conductance mechanosensitive channel
  • Ligand: DODECANE
Keywordschimera / mechanosensitive ion channel / MscS-like / MEMBRANE PROTEIN
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / cellular response to osmotic stress / protein homooligomerization / monoatomic ion transmembrane transport / identical protein binding / membrane / plasma membrane
Similarity search - Function
Mechanosensitive ion channel protein YnaI-like / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / Mechanosensitive ion channel MscS, archaea/bacteria type / : / : / 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 protein YnaI-like / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / Mechanosensitive ion channel MscS, archaea/bacteria type / : / : / 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
Low conductance mechanosensitive channel YnaI / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesunidentified (others) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFlegler VJ / Bottcher B / Rasmussen T / Rasmussen A / Hedrich R
Funding support Germany, 1 items
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 15, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51817.png

Downloads & links

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Map

FileDownload / File: emd_51817.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.95 Å/pix.
x 256 pix.
= 242.176 Å		0.95 Å/pix.
x 256 pix.
= 242.176 Å		0.95 Å/pix.
x 256 pix.
= 242.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.6
Minimum - Maximum-15.974246000000001 - 31.778316
Average (Standard dev.)0.000000000006532 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 242.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51817_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51817_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51817_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : A YnaI-MscS chimera in a closed conformation

EntireName: A YnaI-MscS chimera in a closed conformation
Components
  • Complex: A YnaI-MscS chimera in a closed conformation
    • Protein or peptide: Low conductance mechanosensitive channel YnaI,Small-conductance mechanosensitive channel
  • Ligand: DODECANE

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Supramolecule #1: A YnaI-MscS chimera in a closed conformation

SupramoleculeName: A YnaI-MscS chimera in a closed conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: unidentified (others)

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Macromolecule #1: Low conductance mechanosensitive channel YnaI,Small-conductance m...

MacromoleculeName: Low conductance mechanosensitive channel YnaI,Small-conductance mechanosensitive channel
type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 36.448789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AELFTNNALN LVIIFGSCAA LILMSFWFRR GNRKRKGFLF HAVQFLIYTI IISAVGSIIN YVIENYKLKF ITPGVIDFIC TSLIAVILT IKLFLLINQF EKQQIKKGRD ITSARIMSRI IKITIIVVLV LLYGEHFGVQ TASVIAVLGA AGLAVGLALQ G SLSNLAAG ...String:
AELFTNNALN LVIIFGSCAA LILMSFWFRR GNRKRKGFLF HAVQFLIYTI IISAVGSIIN YVIENYKLKF ITPGVIDFIC TSLIAVILT IKLFLLINQF EKQQIKKGRD ITSARIMSRI IKITIIVVLV LLYGEHFGVQ TASVIAVLGA AGLAVGLALQ G SLSNLAAG VLLVMFRPFR AGEYVDLGGV AGTVLSVQIF STTMRTADGK IIVIPNGKII AGNIINFSRE PVRRNEFIIG VA YDSDIDQ VKQILTNIIQ SEDRILKDRE MTVRLNELGA SSINFVVRVW SNSGDLQNVY WDVLERIKRE FDAAGISFPY PQM DVNFKR V

UniProtKB: Low conductance mechanosensitive channel YnaI, Small-conductance mechanosensitive channel

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Macromolecule #2: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 2 / Number of copies: 21 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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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

Concentration6 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
50.0 mMC8H18N2O4SHEPES
0.03 %C24H46O11DDM
0.1 mg/mlAzolectin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4 s blotting, blot force +25.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 9563 / Average exposure time: 5.94 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3067795
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rld


Details: used 6RLD for MscS part and a portion of closed YnaI obtained in this study
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 311990
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC / Details: heterogeneous refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 76
Output model

PDB-9h2s:
a YnaI-MscS chimera in a closed conformation purified in DDM with additional lipids showing ligand-filled pore and pockets

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