5NKQ

Crystal structure of a dual topology fluoride ion channel.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5fxb


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: 548-551

  • DOI: https://doi.org/10.1038/nature14981
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative fluoride ion transporter CrcB
A, B, C, D
128Bordetella pertussisMutation(s): 0 
Gene Names: crcBBP1217
Membrane Entity: Yes 
UniProt
Find proteins for Q7VYU0 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Explore Q7VYU0 
Go to UniProtKB:  Q7VYU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7VYU0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monobody
E, F, G, H
92Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
N [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
F
Query on F

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth B]
M [auth B]
O [auth C]
J [auth A],
K [auth A],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth D]
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.59α = 109.41
b = 84.06β = 101.4
c = 85.96γ = 101.37
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom102890/Z/13/Z
National Institutes of HealthUnited StatesRO1-GM107023
National Institutes of HealthUnited StatesU54-GM087519
National Institutes of HealthUnited StatesK99-GM-111767

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Author supporting evidence
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description