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 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C6NClick on this verticalbar to view details

This is version 1.4 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: https://doi.org/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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bestrophin-1
A, B, C, D, E
409Gallus gallusMutation(s): 0 
Gene Names: Best1 bestrophin-1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab antibody fragment, light chain
F, H, J, L, N
212Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab antibody fragment, heavy chain
G, I, K, M, O
217Mus musculusMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C6N
Query on C6N

Download Ideal Coordinates CCD File 
CA [auth B],
KA [auth C],
QA [auth D],
V [auth A],
XA [auth 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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth C],
LA [auth D],
P [auth A],
RA [auth E],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth C],
MA [auth D],
S [auth A],
SA [auth E],
X [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth B],
IA [auth C],
JA [auth C],
U [auth A],
WA [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B]
FA [auth C]
GA [auth C]
HA [auth C]
NA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.234 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C6NClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary