7N4T | pdb_00007n4t

Low conductance mechanosensitive channel YnaI

• PDB DOI: https://doi.org/10.2210/pdb7N4T/pdb
• EM Map EMD-24177: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-06-04 Released: 2022-04-20 
• Deposition Author(s): Catalano, C., Ben-Hail, D., Qiu, W., des Georges, A., Guo, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM Structure of Mechanosensitive Channel YnaI Using SMA2000: Challenges and Opportunities.

Catalano, C., Ben-Hail, D., Qiu, W., Blount, P., des Georges, A., Guo, Y.

(2021) Membranes (Basel) 11

• PubMed: 34832078 
• DOI: https://doi.org/10.3390/membranes11110849
• Primary Citation Related Structures: 
  7N4T


• PubMed Abstract: 
  

  Mechanosensitive channels respond to mechanical forces exerted on the cell membrane and play vital roles in regulating the chemical equilibrium within cells and their environment. High-resolution structural information is required to understand the gating mechanisms of mechanosensitive channels. Protein-lipid interactions are essential for the structural and functional integrity of mechanosensitive channels, but detergents cannot maintain the crucial native lipid environment for purified mechanosensitive channels. Recently, detergent-free systems have emerged as alternatives for membrane protein structural biology. This report shows that while membrane-active polymer, SMA2000, could retain some native cell membrane lipids on the transmembrane domain of the mechanosensitive-like YnaI channel, the complete structure of the transmembrane domain of YnaI was not resolved. This reveals a significant limitation of SMA2000 or similar membrane-active copolymers. This limitation may come from the heterogeneity of the polymers and nonspecific interactions between the polymers and the relatively large hydrophobic pockets within the transmembrane domain of YnaI. However, this limitation offers development opportunities for detergent-free technology for challenging membrane proteins.

---

Organizational Affiliation: 
• Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298-0540, USA.
Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23298-0113, USA.
Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10017, USA.
Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.
Department of Chemistry & Biochemistry, City College of New York, New York, NY 10017, USA.
Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10031, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 276.75 kDa 
• Atom Count: 12,887 
• Modeled Residue Count: 1,603 
• Deposited Residue Count: 2,401 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low conductance mechanosensitive channel YnaI	A, B, C, D, E, F, G	343	Escherichia coli 'BL21-Gold(DE3)pLysS AG	Mutation(s): 0  Gene Names: ynaI, b1330, JW1323 Membrane Entity: Yes
UniProt
Find proteins for P0AEB5 (Escherichia coli (strain K12)) Explore P0AEB5  Go to UniProtKB:  P0AEB5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEE (Subject of Investigation/LOI)	H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C41 H78 N O8 P MWRBNPKJOOWZPW-NYVOMTAGSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-20 
Deposition Author(s): Catalano, C., Ben-Hail, D., Qiu, W., des Georges, A., Guo, Y.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM132329
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM133598

Revision History  

• Version 1.0: 2022-04-20
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection, Refinement description