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- EMDB-47553: Cryo-EM structure of MscS/YnaI chimera in DOPC nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-47553
TitleCryo-EM structure of MscS/YnaI chimera in DOPC nanodiscs
Map data
Sample
  • Complex: MscS/YnaI chimera
    • Protein or peptide: MscS/YnaI chimera
KeywordsMechanosensitive / MEMBRANE PROTEIN
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / 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 speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsHiotis G / Will N / Walz T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM144581 United States
CitationJournal: Nat Commun / Year: 2025
Title: Lipid interactions and gating hysteresis suggest a physiological role for mechanosensitive channel YnaI.
Authors: Nathan Will / Giorgos Hiotis / Yoshitaka Nakayama / Gabriella Angiulli / Zijing Zhou / Charles D Cox / Boris Martinac / Thomas Walz /
Abstract: YnaI is a member of the family of bacterial MscS (mechanosensitive channel of small conductance)-like channels. Channel gating upon hypoosmotic stress and the role of lipids in this process have been ...YnaI is a member of the family of bacterial MscS (mechanosensitive channel of small conductance)-like channels. Channel gating upon hypoosmotic stress and the role of lipids in this process have been extensively studied for MscS, but are less well understood for YnaI, which features two additional transmembrane helices. Here, we combined cryogenic electron microscopy, molecular dynamics simulations and patch-clamp electrophysiology to advance our understanding of YnaI. The two additional helices move the lipid-filled hydrophobic pockets in YnaI further away from the lipid bilayer and change the function of the pocket lipids from being a critical gating element in MscS to being more of a structural element in YnaI. Unlike MscS, YnaI shows pronounced gating hysteresis and remains open to a substantially lower membrane tension than is needed to initially open the channel. Thus, at near-lytic membrane tension, both MscL and YnaI will open, but while MscL has a large pore and must close quickly to minimize loss of essential metabolites, YnaI only conducts ions and can thus remain open for longer to continue to facilitate pressure equilibration across the membrane.
History
DepositionOct 29, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47553.png

Downloads & links

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Map

FileDownload / File: emd_47553.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.36982456 - 1.2877355
Average (Standard dev.)0.0022536812 (±0.03057116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47553_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47553_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : MscS/YnaI chimera

EntireName: MscS/YnaI chimera
Components
  • Complex: MscS/YnaI chimera
    • Protein or peptide: MscS/YnaI chimera

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Supramolecule #1: MscS/YnaI chimera

SupramoleculeName: MscS/YnaI chimera / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: MscS/YnaI chimera

MacromoleculeName: MscS/YnaI chimera / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 34.443734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEDLNVVDSI NGAGSWLVAN QALLLSYAVN IDFICTSLIA VILTIKLFLL INQFEKQQIK KGRDITSARI MSRIIKITII VVLVLLYGE HFGMSLSGLL TFGGIGGLAV GMAGKDILSN FFSGIMLYFD RPFSIGDWIR SPDRNIEGTV AEIGWRITKI T TFDNRPLY ...String:
MEDLNVVDSI NGAGSWLVAN QALLLSYAVN IDFICTSLIA VILTIKLFLL INQFEKQQIK KGRDITSARI MSRIIKITII VVLVLLYGE HFGMSLSGLL TFGGIGGLAV GMAGKDILSN FFSGIMLYFD RPFSIGDWIR SPDRNIEGTV AEIGWRITKI T TFDNRPLY VPNSLFSSIS VENPGRMTNR RITTTIGLRY EDAAKVGVIV EAVREMLKNH PAIDQRQTLL VYFNQFADSS LN IMVYCFT KTTVWAEWLA AQQDVYLKII DIVQSHGADF AFPSQTLYMD NITPPEQGRA AALEHHHHHH

UniProtKB: Small-conductance mechanosensitive channel, 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 54.76 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 282223
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

6urt


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9e68:
Cryo-EM structure of MscS/YnaI chimera in DOPC nanodiscs

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