9EFZ | pdb_00009efz

Chicken BEST1 bound to GABA in an open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.95 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 pentameric chloride channel BEST1 is activated by extracellular GABA.

Pant, S.Tam, S.W.Long, S.B.

(2025) Proc Natl Acad Sci U S A 122: e2424474122-e2424474122

  • DOI: https://doi.org/10.1073/pnas.2424474122
  • Primary Citation of Related Structures:  
    9EFZ, 9EGM, 9EGQ, 9EGS, 9EGT

  • PubMed Abstract: 

    Bestrophin-1 (BEST1) is a chloride channel expressed in the eye and other tissues of the body. A link between BEST1 and the principal inhibitory neurotransmitter γ -aminobutyric acid (GABA) has been proposed. The most appreciated receptors for extracellular GABA are the GABA B G-protein-coupled receptors and the pentameric GABA A chloride channels, both of which have fundamental roles in the central nervous system. Here, we demonstrate that BEST1 is directly activated by GABA. Through functional studies and atomic-resolution structures of human and chicken BEST1, we identify a GABA binding site on the channel's extracellular side and determine the mechanism by which GABA binding stabilizes opening of the channel's central gate. This same gate, "the neck," is activated by intracellular [Ca 2+ ], indicating that BEST1 is controlled by ligands from both sides of the membrane. The studies demonstrate that BEST1, which shares no structural homology with GABA A receptors, is a GABA-activated chloride channel. The physiological implications of this finding remain to be studied.


  • Organizational Affiliation
    • Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bestrophin 1
A, B, C, D, E
348Gallus gallusMutation(s): 0 
Gene Names: BEST1
Membrane Entity: Yes 
UniProt
Find proteins for A0A8V0ZZU7 (Gallus gallus)
Explore A0A8V0ZZU7 
Go to UniProtKB:  A0A8V0ZZU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8V0ZZU7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ABU (Subject of Investigation/LOI)
Query on ABU

Download Ideal Coordinates CCD File 
H [auth A],
I [auth B],
L [auth C],
O [auth D],
S [auth E]
GAMMA-AMINO-BUTANOIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
P [auth D],
T [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C],
Q [auth D],
R [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection