4RDQ

Calcium-activated chloride channel bestrophin-1, from chicken, in complex with Fab antibody fragments, chloride and calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and insights into the function of a Ca(2+)-activated Cl(-) channel.

Kane Dickson, V.Pedi, L.Long, S.B.

(2014) Nature 516: 213-218

  • DOI: 10.1038/nature13913

  • PubMed Abstract: 
  • Bestrophin calcium-activated chloride channels (CaCCs) regulate the flow of chloride and other monovalent anions across cellular membranes in response to intracellular calcium (Ca(2+)) levels. Mutations in bestrophin 1 (BEST1) cause certain eye disea ...

    Bestrophin calcium-activated chloride channels (CaCCs) regulate the flow of chloride and other monovalent anions across cellular membranes in response to intracellular calcium (Ca(2+)) levels. Mutations in bestrophin 1 (BEST1) cause certain eye diseases. Here we present X-ray structures of chicken BEST1-Fab complexes, at 2.85 Å resolution, with permeant anions and Ca(2+). Representing, to our knowledge, the first structure of a CaCC, the eukaryotic BEST1 channel, which recapitulates CaCC function in liposomes, is formed from a pentameric assembly of subunits. Ca(2+) binds to the channel's large cytosolic region. A single ion pore, approximately 95 Å in length, is located along the central axis and contains at least 15 binding sites for anions. A hydrophobic neck within the pore probably forms the gate. Phenylalanine residues within it may coordinate permeating anions via anion-π interactions. Conformational changes observed near the 'Ca(2+) clasp' hint at the mechanism of Ca(2+)-dependent gating. Disease-causing mutations are prevalent within the gating apparatus.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bestrophin-1
A, B, C, D, E
409Gallus gallusMutation(s): 0 
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
Find proteins for E1C3A0 (Gallus gallus)
Go to Gene View: BEST1
Go to UniProtKB:  E1C3A0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab antibody fragment, light chain
F, H, J, L, N
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab antibody fragment, heavy chain
G, I, K, M, O
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
C6N
Query on C6N

Download SDF File 
Download CCD File 
A, B, C, D, E
6-cyclohexyl-2-(4-cyclohexylbutyl)-2-({[4-O-(alpha-D-glucopyranosyl)-beta-D-glucopyranosyl]oxy}methyl)hexyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
C47 H84 O22
IBVSQWFQEONEKZ-VWHTXWAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 98.540α = 90.00
b = 242.904β = 93.68
c = 172.757γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXrefinement
SHARPphasing
CNSrefinement
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Structure summary
  • Version 1.2: 2014-12-24
    Type: Database references
  • Version 1.3: 2019-07-17
    Type: Data collection, Refinement description