small conductance mechanosensitive channel YbiO

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


The MscS-like channel YnaI has a gating mechanism based on flexible pore helices.

Flegler, V.J.Rasmussen, A.Rao, S.Wu, N.Zenobi, R.Sansom, M.S.P.Hedrich, R.Rasmussen, T.Bottcher, B.

(2020) Proc Natl Acad Sci U S A 117: 28754-28762

  • DOI: https://doi.org/10.1073/pnas.2005641117
  • Primary Citation of Related Structures:  
    6ZYD, 6ZYE, 7A46

  • PubMed Abstract: 

    The mechanosensitive channel of small conductance (MscS) is the prototype of an evolutionarily diversified large family that fine-tunes osmoregulation but is likely to fulfill additional functions. Escherichia coli has six osmoprotective paralogs with different numbers of transmembrane helices. These helices are important for gating and sensing in MscS but the role of the additional helices in the paralogs is not understood. The medium-sized channel YnaI was extracted and delivered in native nanodiscs in closed-like and open-like conformations using the copolymer diisobutylene/maleic acid (DIBMA) for structural studies. Here we show by electron cryomicroscopy that YnaI has an extended sensor paddle that during gating relocates relative to the pore concomitant with bending of a GGxGG motif in the pore helices. YnaI is the only one of the six paralogs that has this GGxGG motif allowing the sensor paddle to move outward. Access to the pore is through a vestibule on the cytosolic side that is fenestrated by side portals. In YnaI, these portals are obstructed by aromatic side chains but are still fully hydrated and thus support conductance. For comparison with large-sized channels, we determined the structure of YbiO, which showed larger portals and a wider pore with no GGxGG motif. Further in silico comparison of MscS, YnaI, and YbiO highlighted differences in the hydrophobicity and wettability of their pores and vestibule interiors. Thus, MscS-like channels of different sizes have a common core architecture but show different gating mechanisms and fine-tuned conductive properties.

  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, OX1 3QU Oxford, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative transport protein
A, B, C, D, E
A, B, C, D, E, F, G
765Escherichia coliMutation(s): 0 
Gene Names: ybiOBN17_06071
Membrane Entity: Yes 
Find proteins for P75783 (Escherichia coli (strain K12))
Explore P75783 
Go to UniProtKB:  P75783
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75783
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyBo1150/15-1
German Research Foundation (DFG)GermanyINST 93/903-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references