9MLV | pdb_00009mlv

Structure of acid-sensing ion channel 5 without calcium, closed

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-12-19 Released: 2025-09-24 
  • Deposition Author(s): Freitas, M.M., Gouaux, E.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

The bile acid-sensitive ion channel is gated by Ca 2+ -dependent conformational changes in the transmembrane domain.

Freitas, M.M.Gouaux, E.

(2025) Nat Commun 16: 6746-6746

  • DOI: https://doi.org/10.1038/s41467-025-62038-9
  • Primary Citation of Related Structures:  
    9MKY, 9MKZ, 9MLV

  • PubMed Abstract: 

    The bile acid-sensitive ion channel (BASIC) is the least understood member of the mammalian epithelial Na + channel/degenerin (ENaC/DEG) superfamily of ion channels, which are involved in a variety of physiological processes. While some members of this superfamily, including BASIC, are inhibited by extracellular Ca 2+ (Ca 2+ o ), the molecular mechanism underlying Ca 2+ modulation remains unclear. Here, by determining the structure of human BASIC (hBASIC) in the presence and absence of Ca 2+ using single-particle cryo-electron microscopy (cryo-EM), we reveal Ca 2+ -dependent conformational changes in the transmembrane domain and β-linkers. Electrophysiological experiments further show that a glutamate residue in the extracellular vestibule of the pore underpins the Ca 2+ -binding site, whose occupancy determines the conformation of the pore and therefore ion flow through the channel. These results reveal the molecular principles governing gating of BASIC and its regulation by Ca 2+ ions, demonstrating that Ca 2+ ions modulate BASIC function via changes in protein conformation rather than solely from a pore-block, as proposed for other members of this superfamily.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health and Science University, 3232 SW Research Drive, Portland, OR, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acid-sensing ion channel 5A,
B [auth C],
C [auth B]
505Homo sapiensMutation(s): 0 
Gene Names: ASIC5ACCN5HINAC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY37 (Homo sapiens)
Explore Q9NY37 
Go to UniProtKB:  Q9NY37
PHAROS:  Q9NY37
GTEx:  ENSG00000256394 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NY37
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.2.1
RECONSTRUCTIONcryoSPARC3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesF31NS120713
National Science Foundation (NSF, United States)United States1000271223
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release