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- EMDB-20508: MscS Nanodisc with N-terminal His-Tag -

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Basic information

Entry
Database: EMDB / ID: EMD-20508
TitleMscS Nanodisc with N-terminal His-Tag
Map dataMscS ND with N-terminal His-Tag
Sample
  • Complex: Mechanosensitive Channel of Small Conductance
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: HEXADECANE
KeywordsMscS / Nanodisc / Mechanosensitive Channel of Small Conductance / Mechanosensitive / Channel / 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 MscS, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / 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, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / 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) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsReddy BG / Perozo E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM133191 United States
CitationJournal: Elife / Year: 2019
Title: Molecular basis of force-from-lipids gating in the mechanosensitive channel MscS.
Authors: Bharat Reddy / Navid Bavi / Allen Lu / Yeonwoo Park / Eduardo Perozo /
Abstract: Prokaryotic mechanosensitive (MS) channels open by sensing the physical state of the membrane. As such, lipid-protein interactions represent the defining molecular process underlying ...Prokaryotic mechanosensitive (MS) channels open by sensing the physical state of the membrane. As such, lipid-protein interactions represent the defining molecular process underlying mechanotransduction. Here, we describe cryo-electron microscopy (cryo-EM) structures of the small-conductance mechanosensitive channel (MscS) in nanodiscs (ND). They reveal a novel membrane-anchoring fold that plays a significant role in channel activation and establish a new location for the lipid bilayer, shifted ~14 Å from previous consensus placements. Two types of lipid densities are explicitly observed. A phospholipid that 'hooks' the top of each TM2-TM3 hairpin and likely plays a role in force sensing, and a bundle of acyl chains occluding the permeation path above the L105 cuff. These observations reshape our understanding of force-from-lipids gating in MscS and highlight the key role of allosteric interactions between TM segments and phospholipids bound to key dynamic components of the channel.
History
DepositionJul 23, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseJan 8, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0092
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0092
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pwn
  • Surface level: 0.0092
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20508.png

Downloads & links

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Map

FileDownload / File: emd_20508.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMscS ND with N-terminal His-Tag
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0092 / Movie #1: 0.0092
Minimum - Maximum-0.027026389 - 0.07315832
Average (Standard dev.)0.000025131407 (±0.002106049)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z272.384272.384272.384
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0270.0730.000

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Supplemental data

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Half map: Unfiltered Half Map 2

Fileemd_20508_half_map_1.map
AnnotationUnfiltered Half Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered Half Map 1

Fileemd_20508_half_map_2.map
AnnotationUnfiltered Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mechanosensitive Channel of Small Conductance

EntireName: Mechanosensitive Channel of Small Conductance
Components
  • Complex: Mechanosensitive Channel of Small Conductance
    • Protein or peptide: Small-conductance mechanosensitive channel
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: HEXADECANE

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Supramolecule #1: Mechanosensitive Channel of Small Conductance

SupramoleculeName: Mechanosensitive Channel of Small Conductance / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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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 (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 33.094258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MEDLNVVDSI NGAGSWLVAN QALLLSYAVN IVAALAIIIV GLIIARMISN AVNRLMISRK IDATVADFL SALVRYGIIA FTLIAALGRV GVQTASVIAV LGAAGLAVGL ALQGSLSNLA AGVLLVMFRP FRAGEYVDLG G VAGTVLSV ...String:
MGSSHHHHHH SSGLVPRGSH MEDLNVVDSI NGAGSWLVAN QALLLSYAVN IVAALAIIIV GLIIARMISN AVNRLMISRK IDATVADFL SALVRYGIIA FTLIAALGRV GVQTASVIAV LGAAGLAVGL ALQGSLSNLA AGVLLVMFRP FRAGEYVDLG G VAGTVLSV QIFSTTMRTA DGKIIVIPNG KIIAGNIINF SREPVRRNEF IIGVAYDSDI DQVKQILTNI IQSEDRILKD RE MTVRLNE LGASSINFVV RVWSNSGDLQ NVYWDVLERI KREFDAAGIS FPYPQMDVNF KRVKEDKAA

UniProtKB: Small-conductance mechanosensitive channel

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 7 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 3 / Number of copies: 7 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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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

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: 22C. Blot Force 3 for 3 seconds. Double application with a blotting between applications..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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: PDB ENTRY
PDB model - PDB ID:

2oau

Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 372870
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6pwn:
MscS Nanodisc with N-terminal His-Tag

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