5A43 | pdb_00005a43

Crystal structure of a dual topology fluoride ion channel.

• PDB DOI: https://doi.org/10.2210/pdb5A43/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli S88, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2015-06-04 Released: 2015-09-02 
• Deposition Author(s): Stockbridge, R.B., Kolmakova-Partensky, L., Shane, T., Koide, A., Koide, S., Miller, C., Newstead, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.264 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

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

• PubMed: 26344196 
• DOI: https://doi.org/10.1038/nature14981
• Primary Citation Related Structures: 
  5A40, 5A43, 5NKQ


• 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 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.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA.
Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QU, UK.
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.97 kDa 
• Atom Count: 3,481 
• Modeled Residue Count: 442 
• Deposited Residue Count: 444 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE FLUORIDE ION TRANSPORTER CRCB	A, B	126	Escherichia coli S88	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B7LI20 (Escherichia coli O45:K1 (strain S88 / ExPEC)) Explore B7LI20  Go to UniProtKB:  B7LI20

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MONOBODIES	C, D	96	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMU	F [auth A], I [auth B], J [auth C]	DECYL-BETA-D-MALTOPYRANOSIDE C22 H42 O11 WOQQAWHSKSSAGF-WXFJLFHKSA-N
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
F	E [auth A], H [auth B]	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.264 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.42	α = 90
b = 87.42	β = 90
c = 146.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Stockbridge, R.B., Kolmakova-Partensky, L., Shane, T., Koide, A., Koide, S., Miller, C., Newstead, S.

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2015-09-23
  Changes: Database references
• Version 1.2: 2015-09-30
  Changes: Database references
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary