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- EMDB-30713: Mechanosensitive channel MscS K180R mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-30713
TitleMechanosensitive channel MscS K180R mutant
Map data
Sample
  • Complex: Heptameric MscS K180R
    • Protein or peptide: Mechanosensitive ion channel MscS
KeywordsIon channel / membrane protein
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 speciesPseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWu J / Ke M
CitationJournal: To Be Published
Title: Mechanosensitive channel MscS K180R mutant
Authors: Wu J / Ke M
History
DepositionNov 30, 2020-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dlu
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30713.png

Downloads & links

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Map

FileDownload / File: emd_30713.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-3.800723 - 6.6193953
Average (Standard dev.)-0.005274393 (±0.17143877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 260.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z260.880260.880260.880
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-3.8016.619-0.005

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Supplemental data

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Half map: #1

Fileemd_30713_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_30713_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 : Heptameric MscS K180R

EntireName: Heptameric MscS K180R
Components
  • Complex: Heptameric MscS K180R
    • Protein or peptide: Mechanosensitive ion channel MscS

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Supramolecule #1: Heptameric MscS K180R

SupramoleculeName: Heptameric MscS K180R / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Mechanosensitive ion channel MscS

MacromoleculeName: Mechanosensitive ion channel MscS / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Molecular weightTheoretical: 29.870738 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MELNYDRLVQ QTESWLPIVL EYSGKVALAL LTLAIGWWLI NTLTGRVGGL LARRSVDRTL QGFVGSLVSI VLKILLVVSV ASMIGIQTT SFVAAIGAAG LAIGLALQGS LANFAGGVLI LLFRPFKVGD WIEAQGVAGT VDSILIFHTV LRSGDNKRII V PNGALSNG ...String:
MELNYDRLVQ QTESWLPIVL EYSGKVALAL LTLAIGWWLI NTLTGRVGGL LARRSVDRTL QGFVGSLVSI VLKILLVVSV ASMIGIQTT SFVAAIGAAG LAIGLALQGS LANFAGGVLI LLFRPFKVGD WIEAQGVAGT VDSILIFHTV LRSGDNKRII V PNGALSNG TVTNYSAEPV RRVIFDVGID YDADLKNAQN ILLAMADDPR VLKDPAPVAV VSNLGESAIT LSLRVWVKNA DY WDVMFMF NEKARDALGK EGIGIPFPQR VVKVVQGAMA D

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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 158968
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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