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- EMDB-51489: Sub-open structure of the mechanosensitive channel YbiO -

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Basic information

Entry
Database: EMDB / ID: EMD-51489
TitleSub-open structure of the mechanosensitive channel YbiO
Map data
Sample
  • Complex: MscS-like core of YbiO in GDN/CHS detergent
    • Protein or peptide: Mechanosensitive channel protein
KeywordsMechanosensitive / MscS-like / YbiO / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / plasma membrane
Similarity search - Function
: / Mechanosensitive ion channel, transmembrane helix 1 / Mechanosensitive ion channel YbiO / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS ...: / Mechanosensitive ion channel, transmembrane helix 1 / Mechanosensitive ion channel YbiO / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / 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
Mechanosensitive channel protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsLane BJ / Pliotas C
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S018069/1 United Kingdom
Wellcome Trust219999/Z/19/Z United Kingdom
CitationJournal: Structure / Year: 2025
Title: The mechanosensitive channel YbiO has a conductance equivalent to the largest gated pore.
Authors: Benjamin J Lane / Mariangela Dionysopoulou / Nana Yan / Jonathan D Lippiat / Stephen P Muench / Christos Pliotas /
Abstract: Bacterial mechanosensitive channels are divided into large (MscL) and small (MscS-like) conductance families. The function of MscS and MscL is to protect cells against osmotic shock by acting as ...Bacterial mechanosensitive channels are divided into large (MscL) and small (MscS-like) conductance families. The function of MscS and MscL is to protect cells against osmotic shock by acting as pressure safety valves. Within the MscS-like family, E. coli encodes much larger channels, such as YbiO, MscK, and MscM, but their physiological role remains unclear. Compared to MscL their conductances are reported as 3-10 times lower. We show that YbiO can achieve a conductance of ∼3 nS, and an equivalent pore opening of > 25 Å in diameter, equaling the known largest gated pore, MscL. We determine a cryoelectron microscopy (cryo-EM) structure of YbiO in a sub-open conformation, demonstrating the existence of multiple substates. One substate is consistent with the pore opening extent of our structure and the other matches states previously thought to resemble full openings. Our findings demonstrate surprising capabilities, hinting at new physiological roles for YbiO and potentially other MscS-like channels.
History
DepositionSep 4, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51489.png

Downloads & links

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Map

FileDownload / File: emd_51489.map.gz / Format: CCP4 / Size: 729 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.)
0.74 Å/pix.
x 576 pix.
= 426.24 Å		0.74 Å/pix.
x 576 pix.
= 426.24 Å		0.74 Å/pix.
x 576 pix.
= 426.24 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.1621696 - 0.760477
Average (Standard dev.)0.0023861746 (±0.03301004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 426.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_51489_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_51489_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51489_half_map_2.map
Projections & Slices
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Sample components

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Entire : MscS-like core of YbiO in GDN/CHS detergent

EntireName: MscS-like core of YbiO in GDN/CHS detergent
Components
  • Complex: MscS-like core of YbiO in GDN/CHS detergent
    • Protein or peptide: Mechanosensitive channel protein

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Supramolecule #1: MscS-like core of YbiO in GDN/CHS detergent

SupramoleculeName: MscS-like core of YbiO in GDN/CHS detergent / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Mechanosensitive channel protein

MacromoleculeName: Mechanosensitive channel protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 83.047555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRWILFILFC LLGAPAHAVS IPGVTTTTTT DSTTEPAPEP DIEQKKAAYG ALADVLDNDT SRKELIDQLR TVAATPPAEP VPKIVPPTL VEEQTVLQKV TEVSRHYGEA LSARFGQLYR NITGSPHKPF NPQTFSNALT HFSMLAVLVF GFYWLIRLCA L PLYRKMGQ ...String:
MRWILFILFC LLGAPAHAVS IPGVTTTTTT DSTTEPAPEP DIEQKKAAYG ALADVLDNDT SRKELIDQLR TVAATPPAEP VPKIVPPTL VEEQTVLQKV TEVSRHYGEA LSARFGQLYR NITGSPHKPF NPQTFSNALT HFSMLAVLVF GFYWLIRLCA L PLYRKMGQ WARQKNRERS NWLQLPAMII GAFIIDLLLL ALTLFVGQVL SDNLNAGSRT IAFQQSLFLN AFALIEFFKA VL RLIFCPN VAELRPFTIQ DESARYWSRR LSWLSSLIGY GLIVAVPIIS NQVNVQIGAL ANVIIMLCMT VWALYLIFRN KKE ITQHLL NFAEHSLAFF SLFIRAFALV WHWLASAYFI VLFFFSLFDP GNSLKFMMGA TVRSLAIIGI AAFVSGMFSR WLAK TITLS PHTQRNYPEL QKRLNGWLSA ALKTARILTV CVAVMLLLSA WGLFDFWNWL QNGAGQKTVD ILIRIALILF FSAVG WTVL ASLIENRLAS DIHGRPLPSA RTRTLLTLFR NALAVIISTI TIMIVLSEIG VNIAPLLAGA GALGLAISFG SQTLVK DII TGVFIQFENG MNTGDLVTIG PLTGTVERMS IRSVGVRQDT GAYHIIPWSS ITTFANFVRG IGSVVANYDV DRHEDAD KA NQALKDAVAE LMENEEIRGL IIGEPNFAGI VGLSNTAFTL RVSFTTLPLK QWTVRFALDS QVKKHFDLAG VRAPVQTY Q VLPAPGATPA EPLPPGEPTL LEHHHHHH

UniProtKB: Mechanosensitive channel protein

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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

Concentration1.1 mg/mL
BufferpH: 7.4
GridMaterial: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 66.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 147935
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 131625 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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