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 
  • R-Value Observed: 0.218 

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
  • Primary Citation of Related Structures:  
    4RDQ

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bestrophin-1ABCDE409Gallus gallusMutation(s): 0 
Gene Names: Best1 bestrophin-1BEST1
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)
Explore E1C3A0 
Go to UniProtKB:  E1C3A0
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab antibody fragment, heavy chainGIKMO217Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab antibody fragment, light chainFHJLN212Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C6N
Query on C6N

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
GOL
Query on GOL

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A, B, C, D, E
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B, C, D, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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

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A, B, C, D, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.54α = 90
b = 242.904β = 93.68
c = 172.757γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SHARPphasing
CNSrefinement
REFMACrefinement
CBASSdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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