9GO3 | pdb_00009go3

Sub-open structure of the mechanosensitive channel YbiO


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The mechanosensitive channel YbiO has a conductance equivalent to the largest gated pore.

Lane, B.J.Dionysopoulou, M.Yan, N.Lippiat, J.D.Muench, S.P.Pliotas, C.

(2025) Structure 33: 652-662.e3

  • DOI: https://doi.org/10.1016/j.str.2025.01.014
  • Primary Citation of Related Structures:  
    9GO3

  • PubMed Abstract: 

    Bacterial mechanosensitive channels are divided into large (MscL) and small (MscS-like) conductance families. The function of MscS and MscL is to protect cells against osmotic shock by acting as pressure safety valves. Within the MscS-like family, E. coli encodes much larger channels, such as YbiO, MscK, and MscM, but their physiological role remains unclear. Compared to MscL their conductances are reported as 3-10 times lower. We show that YbiO can achieve a conductance of ∼3 nS, and an equivalent pore opening of > 25 Å in diameter, equaling the known largest gated pore, MscL. We determine a cryoelectron microscopy (cryo-EM) structure of YbiO in a sub-open conformation, demonstrating the existence of multiple substates. One substate is consistent with the pore opening extent of our structure and the other matches states previously thought to resemble full openings. Our findings demonstrate surprising capabilities, hinting at new physiological roles for YbiO and potentially other MscS-like channels.


  • Organizational Affiliation
    • Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; Aston Institute for Membrane Excellence, Aston University, Birmingham B4 7ET, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mechanosensitive channel protein
A, B, C, D, E
A, B, C, D, E, F, G
749Escherichia coliMutation(s): 0 
Gene Names: 
Membrane Entity: Yes 
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S018069/1
Wellcome TrustUnited Kingdom219999/Z/19/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection
  • Version 1.2: 2025-08-20
    Changes: Data collection, Database references