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- EMDB-51897: YnaI in its open conformation, purified in DDM, C1 processed -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-51897
TitleYnaI in its open conformation, purified in DDM, C1 processed
Map data
Sample
  • Complex: E. coli YnaI in its open conformation
    • Protein or peptide: YnaI
Keywordsmechanosensitive ion channel of E. coli / MscS-like / MEMBRANE PROTEIN
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
Low conductance mechanosensitive channel YnaI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 23, 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_51897.png

Downloads & links

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Map

FileDownload / File: emd_51897.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.4
Minimum - Maximum-18.060815999999999 - 31.751553000000001
Average (Standard dev.)0.0070139663 (±0.8705043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
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_51897_msk_1.map
Projections & Slices
AxesZYX

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Additional map: unsharpened map

Fileemd_51897_additional_1.map
Annotationunsharpened map
Projections & Slices
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Half map: #1

Fileemd_51897_half_map_1.map
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Half map: #2

Fileemd_51897_half_map_2.map
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Sample components

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Entire : E. coli YnaI in its open conformation

EntireName: E. coli YnaI in its open conformation
Components
  • Complex: E. coli YnaI in its open conformation
    • Protein or peptide: YnaI

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Supramolecule #1: E. coli YnaI in its open conformation

SupramoleculeName: E. coli YnaI in its open conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: YnaI

MacromoleculeName: YnaI / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MIAELFTNNA LNLVIIFGSC AALILMSFWF RRGNRKRKGF LFHAVQFLIY TIIISAVGSI INYVIENYK LKFITPGVID FICTSLIAVI LTIKLFLLIN QFEKQQIKKG RDITSARIMS R IIKITIIV VLVLLYGEHF GMSLSGLLTF GGIGGLAVGM AGKDILSNFF ...String:
MIAELFTNNA LNLVIIFGSC AALILMSFWF RRGNRKRKGF LFHAVQFLIY TIIISAVGSI INYVIENYK LKFITPGVID FICTSLIAVI LTIKLFLLIN QFEKQQIKKG RDITSARIMS R IIKITIIV VLVLLYGEHF GMSLSGLLTF GGIGGLAVGM AGKDILSNFF SGIMLYFDRP FS IGDWIRS PDRNIEGTVA EIGWRITKIT TFDNRPLYVP NSLFSSISVE NPGRMTNRRI TTT IGLRYE DAAKVGVIVE AVREMLKNHP AIDQRQTLLV YFNQFADSSL NIMVYCFTKT TVWA EWLAA QQDVYLKIID IVQSHGADFA FPSQTLYMDN ITPPEQGRLE HHHHHH

UniProtKB: Low conductance mechanosensitive channel YnaI

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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
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
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: 9866 / Average exposure time: 3.39 sec. / Average electron dose: 40.0 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: 1.8 µm / Nominal defocus min: 1.0 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: 2829312
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: this publication
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Details: relaxed C7 symmetry / Number images used: 180381
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 38

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