5A43

Crystal structure of a dual topology fluoride ion channel.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of a Double-Barrelled Fluoride Ion Channel.

Stockbridge, R.B.Kolmakova-Partensky, L.Shane, T.Koide, A.Koide, S.Miller, C.Newstead, S.

(2015) Nature 525: 548

  • DOI: 10.1038/nature14981
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To contend with hazards posed by environmental fluoride, microorganisms export this anion through F(-)-specific ion channels of the Fluc family. Since the recent discovery of Fluc channels, numerous idiosyncratic features of these proteins have been ...

    To contend with hazards posed by environmental fluoride, microorganisms export this anion through F(-)-specific ion channels of the Fluc family. Since the recent discovery of Fluc channels, numerous idiosyncratic features of these proteins have been unearthed, including strong selectivity for F(-) over Cl(-) and dual-topology dimeric assembly. To understand the chemical basis for F(-) permeation and how the antiparallel subunits convene to form a F(-)-selective pore, here we solve the crystal structures of two bacterial Fluc homologues in complex with three different monobody inhibitors, with and without F(-) present, to a maximum resolution of 2.1 Å. The structures reveal a surprising 'double-barrelled' channel architecture in which two F(-) ion pathways span the membrane, and the dual-topology arrangement includes a centrally coordinated cation, most likely Na(+). F(-) selectivity is proposed to arise from the very narrow pores and an unusual anion coordination that exploits the quadrupolar edges of conserved phenylalanine rings.


    Organizational Affiliation

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE FLUORIDE ION TRANSPORTER CRCB
A, B
126Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: crcB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Fluc Family
Protein: 
Fluc F- ion channel homolog in complex with Bpe-S7 monobody
Find proteins for B7LI20 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7LI20
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MONOBODIES
C, D
96N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F
Query on F

Download SDF File 
Download CCD File 
A, B
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DMU
Query on DMU

Download SDF File 
Download CCD File 
A, B, C
DECYL-BETA-D-MALTOPYRANOSIDE
DECYLMALTOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.224 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 87.420α = 90.00
b = 87.420β = 90.00
c = 146.810γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references
  • Version 1.2: 2015-09-30
    Type: Database references