9DYL

BEST1 + PABA open state

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

  • Deposited: 2024-10-14 Released: 2025-01-08 
  • Deposition Author(s): Owji, A.P., Kittredge, A., Zhang, Y., Yang, T.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Eye Institute (NIH/NEI), Other private, Simons Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Neurotransmitter-bound bestrophin channel structures reveal small molecule drug targeting sites for disease treatment.

Owji, A.P.Dong, J.Kittredge, A.Wang, J.Zhang, Y.Yang, T.

(2024) Nat Commun 15: 10766-10766

  • DOI: https://doi.org/10.1038/s41467-024-54938-z
  • Primary Citation of Related Structures:  
    9DYJ, 9DYK, 9DYL, 9DYM, 9DYN

  • PubMed Abstract: 

    Best1 and Best2 are two members of the bestrophin family of anion channels critically involved in the prevention of retinal degeneration and maintenance of intraocular pressure, respectively. Here, we solved glutamate- and γ-aminobutyric acid (GABA)-bound Best2 structures, which delineate an intracellular glutamate binding site and an extracellular GABA binding site on Best2, respectively, identified extracellular GABA as a permeable activator of Best2, and elucidated the co-regulation of Best2 by glutamate, GABA and glutamine synthetase in vivo. We further identified multiple small molecules as activators of the bestrophin channels. Extensive analyses were carried out for a potent activator, 4-aminobenzoic acid (PABA): PABA-bound Best1 and Best2 structures are solved and illustrate the same binding site as in GABA-bound Best2; PABA treatment rescues the functional deficiency of patient-derived Best1 mutations. Together, our results demonstrate the mechanism and potential of multiple small molecule candidates as clinically applicable drugs for bestrophin-associated diseases/conditions.


  • Organizational Affiliation

    Department of Ophthalmology, Columbia University, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bestrophin-1A,
B [auth E],
C [auth B],
D,
E [auth C]
585Homo sapiensMutation(s): 0 
Gene Names: BEST1VMD2
UniProt & NIH Common Fund Data Resources
Find proteins for O76090 (Homo sapiens)
Explore O76090 
Go to UniProtKB:  O76090
PHAROS:  O76090
GTEx:  ENSG00000167995 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76090
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAB (Subject of Investigation/LOI)
Query on PAB

Download Ideal Coordinates CCD File 
G [auth A],
I [auth E],
K [auth B],
M [auth D],
O [auth C]
4-AMINOBENZOIC ACID
C7 H7 N O2
ALYNCZNDIQEVRV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
H [auth E],
J [auth B],
L [auth D],
N [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

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 StatesR35GM149252
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM127652
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesR24EY028758
Other privateUnited StatesIrma T. Hirschl Trust CU20-4313
Other privateUnited StatesResearch to Prevent Blindness (RPB) CU22-1892
Simons FoundationUnited StatesSF349247
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM129539

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release