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- EMDB-71089: MscS in Glyco-DIBMA Native Nanodiscs (C1 symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-71089
TitleMscS in Glyco-DIBMA Native Nanodiscs (C1 symmetry)
Map dataSharpened Filtered Map
Sample
  • Complex: MscS in Glyco-DIBMA Native Nanodiscs (C1 symmetry)
    • Protein or peptide: Small-conductance mechanosensitive channel
Keywordsmechanosensitive channel / membrane protein / native nanodisc / polymer / Glyco-DIBMA / cryo-EM / lipid
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / plasma membrane
Similarity search - Function
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 ...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
Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsMoller E / Britt M / Zhou F / Yang H / Anishkin A / Ernst R / Juan VM / Sukharev S / Matthies D
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)Z1A HD008998 United States
National Science Foundation (NSF, United States)DGE 1840340 United States
National Science Foundation (NSF, United States)CHE-1944892/2326678 United States
CitationJournal: To Be Published
Title: The lipid-mediated mechanism of mechanosensitive channel MscS inactivation
Authors: Moller E / Britt M / Zhou F / Yang H / Anishkin A / Ernst R / Juan VM / Sukharev S / Matthies D
History
DepositionJun 7, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71089.png

Downloads & links

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Map

FileDownload / File: emd_71089.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Filtered Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 304.884 Å		0.85 Å/pix.
x 360 pix.
= 304.884 Å		0.85 Å/pix.
x 360 pix.
= 304.884 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8469 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0993
Minimum - Maximum-0.5367964 - 0.88417405
Average (Standard dev.)0.0014284017 (±0.01701189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 304.884 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71089_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local Resolution Filtered Map

Fileemd_71089_additional_1.map
AnnotationLocal Resolution Filtered Map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened Map

Fileemd_71089_additional_2.map
AnnotationUnsharpened Map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71089_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_71089_half_map_2.map
Projections & Slices
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Sample components

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Entire : MscS in Glyco-DIBMA Native Nanodiscs (C1 symmetry)

EntireName: MscS in Glyco-DIBMA Native Nanodiscs (C1 symmetry)
Components
  • Complex: MscS in Glyco-DIBMA Native Nanodiscs (C1 symmetry)
    • Protein or peptide: Small-conductance mechanosensitive channel

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Supramolecule #1: MscS in Glyco-DIBMA Native Nanodiscs (C1 symmetry)

SupramoleculeName: MscS in Glyco-DIBMA Native Nanodiscs (C1 symmetry) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 217 KDa

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Macromolecule #1: Small-conductance mechanosensitive channel

MacromoleculeName: Small-conductance mechanosensitive channel / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 28.718561 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LVANQALLLS YAVNIVAALA IIIVGLIIAR MISNAVNRLM ISRKIDATVA DFLSALVRYG IIAFTLIAAL GRVGVQTASV IAVLGAAGL AVGLALQGSL SNLAAGVLLV MFRPFRAGEY VDLGGVAGTV LSVQIFSTTM RTADGKIIVI PNGKIIAGNI I NFSREPVR ...String:
LVANQALLLS YAVNIVAALA IIIVGLIIAR MISNAVNRLM ISRKIDATVA DFLSALVRYG IIAFTLIAAL GRVGVQTASV IAVLGAAGL AVGLALQGSL SNLAAGVLLV MFRPFRAGEY VDLGGVAGTV LSVQIFSTTM RTADGKIIVI PNGKIIAGNI I NFSREPVR RNEFIIGVAY DSDIDQVKQI LTNIIQSEDR ILKDREMTVR LNELGASSIN FVVRVWSNSG DLQNVYWDVL ER IKREFDA AGISFPYPQM DVNFKRVK

UniProtKB: Small-conductance mechanosensitive channel

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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

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
20.0 mMHEPES
100.0 mMSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 79.0 K / Max: 79.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 20649 / Average exposure time: 2.4 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 3380588
CTF correctionSoftware - Name: cryoSPARC (ver. v3.3.250) / Software - details: Patch CTF estimation (multi) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.250) / Number images used: 368753
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.250) / Software - details: Ab-Initio Reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.250) / Software - details: Non-uniform Refinement (Legacy)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7oo6


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 97.2
Output model

PDB-9p0o:
MscS in Glyco-DIBMA Native Nanodiscs (C1 symmetry)

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