9E63 | pdb_00009e63

Cryo-EM structure of mechanosensitive channel YnaI in DOPC nanodiscs treated with beta-cyclodextrin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Lipid interactions and gating hysteresis suggest a physiological role for mechanosensitive channel YnaI.

Will, N.Hiotis, G.Nakayama, Y.Angiulli, G.Zhou, Z.Cox, C.D.Martinac, B.Walz, T.

(2025) Nat Commun 16: 7472-7472

  • DOI: https://doi.org/10.1038/s41467-025-62805-8
  • Primary Citation of Related Structures:  
    9E62, 9E63, 9E64, 9E65, 9E66, 9E67, 9E68

  • PubMed Abstract: 

    YnaI is a member of the family of bacterial MscS (mechanosensitive channel of small conductance)-like channels. Channel gating upon hypoosmotic stress and the role of lipids in this process have been extensively studied for MscS, but are less well understood for YnaI, which features two additional transmembrane helices. Here, we combined cryogenic electron microscopy, molecular dynamics simulations and patch-clamp electrophysiology to advance our understanding of YnaI. The two additional helices move the lipid-filled hydrophobic pockets in YnaI further away from the lipid bilayer and change the function of the pocket lipids from being a critical gating element in MscS to being more of a structural element in YnaI. Unlike MscS, YnaI shows pronounced gating hysteresis and remains open to a substantially lower membrane tension than is needed to initially open the channel. Thus, at near-lytic membrane tension, both MscL and YnaI will open, but while MscL has a large pore and must close quickly to minimize loss of essential metabolites, YnaI only conducts ions and can thus remain open for longer to continue to facilitate pressure equilibration across the membrane.


  • Organizational Affiliation

    Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Low conductance mechanosensitive channel YnaI
A, B, C, D, E
A, B, C, D, E, F, G
351Escherichia coliMutation(s): 0 
Gene Names: ynaIb1330JW1323
UniProt
Find proteins for P0AEB5 (Escherichia coli (strain K12))
Explore P0AEB5 
Go to UniProtKB:  P0AEB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEB5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY (Subject of Investigation/LOI)
Query on PTY

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth D],
BA [auth D],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
GA [auth E],
H [auth A],
HA [auth E],
I [auth A],
IA [auth F],
J [auth A],
JA [auth F],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth B],
NA [auth G],
O [auth B],
OA [auth G],
P [auth B],
PA [auth G],
Q [auth B],
R [auth B],
S [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth D],
Y [auth D],
Z [auth D]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM144581

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release