6VX6 | pdb_00006vx6

bestrophin-2 Ca2+-bound state (250 nM Ca2+)

• PDB DOI: https://doi.org/10.2210/pdb6VX6/pdb
• EM Map EMD-21431: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Bos taurus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2020-02-21 Released: 2020-04-08 
• Deposition Author(s): Owji, A.P., Zhao, Q., Ji, C., Kittredge, A., Hopiavuori, A., Fu, Z., Ward, N., Clarke, O., Shen, Y., Zhang, Y., Hendrickson, W.A., Yang, T.
• Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and functional characterization of the bestrophin-2 anion channel.

Owji, A.P., Zhao, Q., Ji, C., Kittredge, A., Hopiavuori, A., Fu, Z., Ward, N., Clarke, O.B., Shen, Y., Zhang, Y., Hendrickson, W.A., Yang, T.

(2020) Nat Struct Mol Biol 27: 382-391

• PubMed: 32251414 
• DOI: https://doi.org/10.1038/s41594-020-0402-z
• Primary Citation Related Structures: 
  6VX5, 6VX6, 6VX7, 6VX8, 6VX9


• PubMed Abstract: 
  

  The bestrophin family of calcium (Ca ²⁺ )-activated chloride (Cl ^- ) channels, which mediate the influx and efflux of monovalent anions in response to the levels of intracellular Ca ²⁺ , comprises four members in mammals (bestrophin 1-4). Here we report cryo-EM structures of bovine bestrophin-2 (bBest2) bound and unbound by Ca ²⁺ at 2.4- and 2.2-Å resolution, respectively. The bBest2 structure highlights four previously underappreciated pore-lining residues specifically conserved in Best2 but not in Best1, illustrating the differences between these paralogs. Structure-inspired electrophysiological analysis reveals that, although the channel is sensitive to Ca ²⁺ , it has substantial Ca ²⁺ -independent activity for Cl ^- , reflecting the opening at the cytoplasmic restriction of the ion conducting pathway even when Ca ²⁺ is absent. Moreover, the ion selectivity of bBest2 is controlled by multiple residues, including those involved in gating.

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Organizational Affiliation: 
• Department of Pharmacology, Columbia University, New York, NY, USA.
Department of Pharmacology and Physiology, University of Rochester, School of Medicine and Dentistry, Rochester, NY, USA.
Eye Center, Renmin Hospital of Wuhan University, Wuhan, China.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.
Eye Center, Renmin Hospital of Wuhan University, Wuhan, China. [e-mail].
Department of Ophthalmology, Columbia University, New York, NY, USA. [e-mail].
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. [e-mail].
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA. [e-mail].
New York Structural Biology Center, New York, NY, USA. [e-mail].
Department of Pharmacology and Physiology, University of Rochester, School of Medicine and Dentistry, Rochester, NY, USA. [e-mail].
Department of Ophthalmology, Columbia University, New York, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 237.36 kDa 
• Atom Count: 15,061 
• Modeled Residue Count: 1,830 
• Deposited Residue Count: 2,050 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bestrophin	A [auth E], B [auth A], C [auth B], D [auth C], E [auth D]	410	Bos taurus	Mutation(s): 0  Gene Names: BEST2 Membrane Entity: Yes
UniProt
Find proteins for E1BF86 (Bos taurus) Explore E1BF86  Go to UniProtKB:  E1BF86

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	F [auth E], H [auth A], I [auth B], J [auth C], K [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Owji, A.P., Zhao, Q., Ji, C., Kittredge, A., Hopiavuori, A., Fu, Z., Ward, N., Clarke, O., Shen, Y., Zhang, Y., Hendrickson, W.A., Yang, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	1F31EY030763
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	EY025290
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	7R01GM127652
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	3R01GM107462

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2020-04-22
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations