|Entry||Database: PDB / ID: 5y4o|
|Title||Cryo-EM structure of MscS channel, YnaI|
|Components||Low conductance mechanosensitive channel YnaI|
|Keywords||MEMBRANE PROTEIN / cryo-EM / MscS / Na/K selective channel|
|Function / homology||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 ...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
|Specimen source||Escherichia coli O157:H7 (bacteria)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å|
|Authors||Zhang, Y. / Yu, J.|
|Funding support||China , 5 items |
|Citation||Journal: Protein Cell / Year: 2018|
Title: A binding-block ion selective mechanism revealed by a Na/K selective channel.
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.
SummaryFull reportAbout validation report
|Date||Deposition: Aug 4, 2017 / Release: Mar 20, 2019|
|Structure viewer||Molecule: |
Downloads & links
A: Low conductance mechanosensitive channel YnaI
B: Low conductance mechanosensitive channel YnaI
C: Low conductance mechanosensitive channel YnaI
D: Low conductance mechanosensitive channel YnaI
E: Low conductance mechanosensitive channel YnaI
F: Low conductance mechanosensitive channel YnaI
G: Low conductance mechanosensitive channel YnaI
Mass: 39621.215 Da / Num. of mol.: 7 / Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ynaI, Z2437, ECs1912
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0AEB6
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: YnaI / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Source (natural)||Organism: Escherichia coli O157:H7 (bacteria)|
|Source (recombinant)||Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)|
|Buffer solution||pH: 6.5|
|Specimen||Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 277 kelvins|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 37 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C7 (7 fold cyclic)|
|3D reconstruction||Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42000 / Symmetry type: POINT|
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