5Y4O

Cryo-EM structure of MscS channel, YnaI


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A binding-block ion selective mechanism revealed by a Na/K selective channel.

Yu, J.Zhang, B.Zhang, Y.Xu, C.Q.Zhuo, W.Ge, J.Li, J.Gao, N.Li, Y.Yang, M.

(2018) Protein Cell 9: 629-639

  • DOI: 10.1007/s13238-017-0465-8

  • PubMed 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 channel gating and ion selectivity are largely unknown ...

    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 Met158 ) 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 Met158 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.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.,Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. Liyang@simm.ac.cn.,Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. maojunyang@tsinghua.edu.cn.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Anesthesiology, Shanghai First Maternity and Infant Hospital, Tongji University school of Medicine, Shanghai, 201203, China.,Department of Chemistry and Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Tsinghua University, Beijing, 100084, China.,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. gaon@pku.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Low conductance mechanosensitive channel YnaI
A, B, C, D, E, F, G
349Escherichia coli O157:H7Mutation(s): 0 
Gene Names: ynaI
Find proteins for P0AEB6 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AEB6
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-08-04 
  • Released Date: 2019-03-20 
  • Deposition Author(s): Zhang, Y., Yu, J.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0501100
Ministry of Science and Technology (China)China2017YFA0504600
National Fund for Distinguished Young ScholarChina31625008
National Natural Science Foundation of ChinaChina21532004
National Natural Science Foundation of ChinaChina31570733

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release