Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Hetero 15-mer - A5B5C5 Pseudo Symmetry: Cyclic - C5  (3D View)
Pseudo Stoichiometry: Hetero 15-mer - A10B5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 473.38 kDa 
• Atom Count: 30705 
• Residue Count: 3945 
• Unique protein chains: 3

5T5N

Calcium-activated chloride channel bestrophin-1 (BEST1), triple mutant: I76A, F80A, F84A; in complex with an Fab antibody fragment, chloride, and calcium

• DOI: 10.2210/pdb5T5N/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Gallus gallus, Mus musculus
• Expression System: Pichia
• Mutation(s): Yes 


• Deposited: 2016-08-31 Released: 2016-11-30 
• Deposition Author(s): Long, S.B., Vaisey, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.218 

Literature

Distinct regions that control ion selectivity and calcium-dependent activation in the bestrophin ion channel.

Vaisey, G., Miller, A.N., Long, S.B.

(2016) Proc Natl Acad Sci U S A 113: E7399-E7408

• PubMed: 27821745 
• DOI: 10.1073/pnas.1614688113
• Primary Citation of Related Structures:  
  5T5N


• PubMed Abstract: 
  

Cytoplasmic calcium (Ca ²⁺ ) activates the bestrophin anion channel, allowing chloride ions to flow down their electrochemical gradient. Mutations in bestrophin 1 (BEST1) cause macular degenerative disorders. Previously, we determined an X-ray structure of chicken BEST1 that revealed the architecture of the channel. Here, we present electrophysiological studies of purified wild-type and mutant BEST1 channels and an X-ray structure of a Ca ²⁺ -independent mutant. From these experiments, we identify regions of BEST1 responsible for Ca ²⁺ activation and ion selectivity. A "Ca ²⁺ clasp" within the channel's intracellular region acts as a sensor of cytoplasmic Ca ²⁺ . Alanine substitutions within a hydrophobic "neck" of the pore, which widen it, cause the channel to be constitutively active, irrespective of Ca ²⁺ . We conclude that the primary function of the neck is as a "gate" that controls chloride permeation in a Ca ²⁺ -dependent manner. In contrast to what others have proposed, we find that the neck is not a major contributor to the channel's ion selectivity. We find that mutation of a cytosolic "aperture" of the pore does not perturb the Ca ²⁺ dependence of the channel or its preference for anions over cations, but its mutation dramatically alters relative permeabilities among anions. The data suggest that the aperture functions as a size-selective filter that permits the passage of small entities such as partially dehydrated chloride ions while excluding larger molecules such as amino acids. Thus, unlike ion channels that have a single "selectivity filter," in bestrophin, distinct regions of the pore govern anion-vs.-cation selectivity and the relative permeabilities among anions.

---

Organizational Affiliation: 

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bestrophin-1 (BEST1)	A, B, C, D, E	409	Gallus gallus	Mutation(s): 3  Gene Names: BEST1
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Channels: Other Ion Channels	Protein:  Bestrophin-1 (BEST1) Ca2+-activated Cl- channel I76A, F80A, F84A mutant
Find proteins for E1C3A0 (Gallus gallus) Explore E1C3A0  Go to UniProtKB:  E1C3A0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab antibody fragment, light chain (10D10)	F, H, J, L, N	212	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab antibody fragment, heavy chain (10D10)	G, I, K, M, O	217	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B, C, D, E	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B, C, D, E	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	A, C, E	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	A, B, C, D, E	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.243	α = 90
b = 243.878	β = 93.84
c = 172.052	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-08-31 
• Released Date: 2016-11-30 
Deposition Author(s): Long, S.B., Vaisey, G.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM110396

Revision History 

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Refinement description
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence