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- EMDB-76009: EcMscM lacking the first periplasmic helical bundle in NaCl in a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-76009
TitleEcMscM lacking the first periplasmic helical bundle in NaCl in a closed conformation
Map dataEMReady sharpened map
Sample
  • Complex: MscM
    • Protein or peptide: Miniconductance mechanosensitive channel MscM
KeywordsMechanosensitive / Ion channel / MscS / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / cellular response to osmotic stress / plasma membrane
Similarity search - Function
Mechanosensitive ion channel MscS, porin domain / Mechanosensitive ion channel inner membrane domain 1 / : / Mechanosensitive ion channel inner membrane domain 1 / Mechanosensitive ion channel porin domain / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site ...Mechanosensitive ion channel MscS, porin domain / Mechanosensitive ion channel inner membrane domain 1 / : / Mechanosensitive ion channel inner membrane domain 1 / Mechanosensitive ion channel porin domain / : / : / 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
Miniconductance mechanosensitive channel MscM
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsHiotis G / 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: 2026
Title: The bacterial mechanosensitive channel MscM gates through concerted changes in its transmembrane and cytoplasmic domains.
Authors: Giorgos Hiotis / Thomas Walz /
Abstract: The mechanosensitive channel of small conductance (MscS) is the founding member of the family of MscS-like channels, which share a structurally conserved core but feature additional structural ...The mechanosensitive channel of small conductance (MscS) is the founding member of the family of MscS-like channels, which share a structurally conserved core but feature additional structural elements that define their specific channel characteristics. Here, we characterize the structure and function of the Escherichia coli mechanosensitive channel of mini conductance (MscM), which features eight additional transmembrane (TM) helices and a large periplasmic domain. Our cryo-EM structures reveal that channel gating involves conformational changes in all domains of MscM. In particular, a cytoplasmic extension of TM7 couples the conformation of the TM domain to that of the cytoplasmic domain, resulting in gating of its lateral fenestrations, where ions enter the channel. Thus, different from all other MscS-like channels studied to date, channel gating in MscM is mediated by its cytoplasmic domain and not the TM domain, which senses changes in membrane tension and operates the cytoplasmic gates.
History
DepositionMar 11, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76009.png

Downloads & links

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Map

FileDownload / File: emd_76009.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMReady sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 450 pix.
= 381.15 Å		0.85 Å/pix.
x 450 pix.
= 381.15 Å		0.85 Å/pix.
x 450 pix.
= 381.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.847 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.1
Minimum - Maximum-0.12441105 - 12.011570000000001
Average (Standard dev.)-0.00012251205 (±0.40365875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 381.15 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_76009_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76009_half_map_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_76009_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MscM

EntireName: MscM
Components
  • Complex: MscM
    • Protein or peptide: Miniconductance mechanosensitive channel MscM

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Supramolecule #1: MscM

SupramoleculeName: MscM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Miniconductance mechanosensitive channel MscM

MacromoleculeName: Miniconductance mechanosensitive channel MscM / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 100.859641 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MRLIITFLMA WCLSWGAYAA TAPDSKQITQ ELEQAKAAKP DLPKDIVAQF KINRELSAAL NQQAQRMDLV ASQQRQAASQ TLQVRQALN TLREQSQWLG SSNLLGEALR AQVARLPEMP KPQQLDTEMA QLRVQRLRYE DLLNKQPLLR QIHQADGQPL T AEQNRILE ...String:
MRLIITFLMA WCLSWGAYAA TAPDSKQITQ ELEQAKAAKP DLPKDIVAQF KINRELSAAL NQQAQRMDLV ASQQRQAASQ TLQVRQALN TLREQSQWLG SSNLLGEALR AQVARLPEMP KPQQLDTEMA QLRVQRLRYE DLLNKQPLLR QIHQADGQPL T AEQNRILE AQLRTQRELL NSLLQGGDTL LLELTKLKVS NGQLEDALKE VNEATHRYLF WTSDVRPMTI AWPLEIAQDL RR LISLDTF SQLGKASVMM LTSKETILPL FGALILVGCS IYSRRYFTRF LERSAAKVGK VTQDHFWLTL RTLFWSILVA SPL PVLWMT LGYGLREAWP YPLAVAIGDG VTATVPLLWV VMICATFARP NGLFIAHFGW PRERVSRGMR YYLMSIGLIV PLIM ALMMF DNLDDREFSG SLGRLCFILI CGALAVVTLS LKKAGIPLYL NKEGSGDNIT NHMLWNMMIG APLVAILASA VGYLA TAQA LLARLETSVA IWFLLLVVYH VIRRWMLIQR RRLAFDRAKH RRAEMLAQRA RGEEEAHHHS SPEGAIEVDE SEVDLD AIS AQSLRLVRSI LMLIALLSVI VLWSEIHSAF GFLENISLWD VTSTVQGVES LEPITLGAVL IAILVFIITT QLVRNLP AL LELAILQHLD LTPGTGYAIT TITKYLLMLI GGLVGFSMIG IEWSKLQWLV AALGVGLGFG LQEIFANFIS GLIILFEK P IRIGDTVTIR DLTGSVTKIN TRATTISDWD RKEIIVPNKA FITEQFINWS LSDSVTRVVL TIPAPADANS EEVTEILLT AARRCSLVID NPAPEVFLVD LQQGIQIFEL RIYAAEMGHR MPLRHEIHQL ILAGFHAHGI DMPFPPFQMR LESLNGKQTG RTLTSAGKG RQAGSLLEVL FQ

UniProtKB: Miniconductance mechanosensitive channel MscM

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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: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
30.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
0.02 mg/mLGDNGlyco-diosgenin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.2 sec. / Average electron dose: 46.84 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: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / 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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 58387
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX
Output model

PDB-11so:
EcMscM lacking the first periplasmic helical bundle in NaCl in a closed conformation

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