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- EMDB-6805: Cryo-EM structure of MscS channel, YnaI -

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Basic information

Entry
Database: EMDB / Id: 6805
TitleCryo-EM structure of MscS channel, YnaI
Map dataYnaI EM map
SampleYnaI
  • Low conductance mechanosensitive channel YnaI
Func homologyMechanosensitive ion channel MscS / Mechanosensitive ion channel MscS, conserved site / LSM domain superfamily / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS domain superfamily / Mechanosensitive ion channel / Uncharacterized protein family UPF0003 signature. / ion transport / transmembrane transport ...Mechanosensitive ion channel MscS / Mechanosensitive ion channel MscS, conserved site / LSM domain superfamily / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS domain superfamily / Mechanosensitive ion channel / Uncharacterized protein family UPF0003 signature. / ion transport / transmembrane transport / integral component of membrane / plasma membrane / Low conductance mechanosensitive channel YnaI
Function and homology information
SourceEscherichia coli O157:H7 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhang Y / Yu J
CitationJournal: Protein Cell / Year: 2018
Title: A binding-block ion selective mechanism revealed by a Na/K selective channel.
P-authors: Jie Yu / Bing Zhang / Yixiao Zhang / Cong-Qiao Xu / Wei Zhuo / Jingpeng Ge / Jun Li / Ning Gao / Yang Li / Maojun Yang /
Abstract: Mechanosensitive (MS) channels are extensively studied membrane protein for maintaining intracellular homeostasis through translocating solutes and ions across the membrane, but its mechanisms of ...Mechanosensitive (MS) channels are extensively studied membrane protein for maintaining intracellular homeostasis through translocating solutes and ions across the membrane, but its mechanisms of channel gating and ion selectivity are largely unknown. Here, we identified the YnaI channel as the Na/K cation-selective MS channel and solved its structure at 3.8 Å by cryo-EM single-particle method. YnaI exhibits low conductance among the family of MS channels in E. coli, and shares a similar overall heptamer structure fold with previously studied MscS channels. By combining structural based mutagenesis, quantum mechanical and electrophysiological characterizations, we revealed that ion selective filter formed by seven hydrophobic methionine (YnaI) in the transmembrane pore determined ion selectivity, and both ion selectivity and gating of YnaI channel were affected by accompanying anions in solution. Further quantum simulation and functional validation support that the distinct binding energies with various anions to YnaI facilitate Na/K pass through, which was defined as binding-block mechanism. Our structural and functional studies provided a new perspective for understanding the mechanism of how MS channels select ions driven by mechanical force.
Validation ReportPDB-ID: 5y4o

SummaryFull reportAbout validation report
DateDeposition: Aug 4, 2017 / Header (metadata) release: Mar 20, 2019 / Map release: Mar 20, 2019 / Last update: Mar 20, 2019

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Strvis

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0745
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0745
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5y4o
  • Surface level: 0.0745
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_6805.map.gz (map file in CCP4 format, 11944 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
1.32 Å/pix.
= 190.08 Å
144 pix
1.32 Å/pix.
= 190.08 Å
144 pix
1.32 Å/pix.
= 190.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.0745 (by author), 0.0745 (movie #1):
Minimum - Maximum-0.28578657 - 0.43834007
Average (Standard dev.)0.0009592251 (0.023311755)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin0.00.00.0
Limit143.0143.0143.0
Spacing144144144
CellA=B=C: 190.08 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z190.080190.080190.080
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.2860.4380.001

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Supplemental data

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Sample components

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Entire YnaI

EntireName: YnaI / Number of components: 2

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Component #1: protein, YnaI

ProteinName: YnaI / Recombinant expression: No
SourceSpecies: Escherichia coli O157:H7 (bacteria)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #2: protein, Low conductance mechanosensitive channel YnaI

ProteinName: Low conductance mechanosensitive channel YnaI / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 39.621215 kDa
SourceSpecies: Escherichia coli O157:H7 (bacteria)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml / Ph: 6.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 85 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 37 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C7 (7 fold cyclic) / Number of projections: 42000
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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