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- EMDB-24390: Small conductance mechanosensitive channel MscS -

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Basic information

Entry
Database: EMDB / ID: EMD-24390
TitleSmall conductance mechanosensitive channel MscS
Map data
Sample
  • Cell: Small conductance mechanosensitive channel MscS
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: PHOSPHATIDYLETHANOLAMINE
Keywordssmall conductance mechanosensitive channel MscS / NCMN / ion channel / membrane protein / TRANSPORT 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
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.4 Å
AuthorsCatalano C / Ben-Hail D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM133598 United States
CitationJournal: To Be Published
Title: Small conductance mechanosensitive channel MscS
Authors: Catalano C / Ben-Hail D / Qiu W / des Georges A / Guo Y
History
DepositionJul 5, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24390.png

Downloads & links

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Map

FileDownload / File: emd_24390.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.011250098 - 0.0433607
Average (Standard dev.)0.00032907046 (±0.0024218108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_24390_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_24390_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 : Small conductance mechanosensitive channel MscS

EntireName: Small conductance mechanosensitive channel MscS
Components
  • Cell: Small conductance mechanosensitive channel MscS
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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Supramolecule #1: Small conductance mechanosensitive channel MscS

SupramoleculeName: Small conductance mechanosensitive channel MscS / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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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 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain: BL21-Gold(DE3)pLysS AG
Molecular weightTheoretical: 30.922898 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MEDLNVVDSI NGAGSWLVAN QALLLSYAVN IVAALAIIIV GLIIARMISN AVNRLMISRK IDATVADFLS ALVRYGIIAF TLIAALGRV GVQTASVIAV LGAAGLAVGL ALQGSLSNLA AGVLLVMFRP FRAGEYVDLG GVAGTVLSVQ IFSTTMRTAD G KIIVIPNG ...String:
MEDLNVVDSI NGAGSWLVAN QALLLSYAVN IVAALAIIIV GLIIARMISN AVNRLMISRK IDATVADFLS ALVRYGIIAF TLIAALGRV GVQTASVIAV LGAAGLAVGL ALQGSLSNLA AGVLLVMFRP FRAGEYVDLG GVAGTVLSVQ IFSTTMRTAD G KIIVIPNG KIIAGNIINF SREPVRRNEF IIGVAYDSDI DQVKQILTNI IQSEDRILKD REMTVRLNEL GASSINFVVR VW SNSGDLQ NVYWDVLERI KREFDAAGIS FPYPQMDVNF KRVKEDKAA

UniProtKB: Small-conductance mechanosensitive channel

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Macromolecule #2: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 7 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
StainingType: NEGATIVE / Material: 2% uranyl acetate
GridModel: UltrAuFoil R0.6/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1352 / Average exposure time: 10.0 sec. / Average electron dose: 61.05 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 500000
Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 275000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

2oau


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7raz:
Small conductance mechanosensitive channel MscS

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