4KJQ

Structure of the CLC-ec1 deltaNC construct in 100mM fluoride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Fluoride-dependent interruption of the transport cycle of a CLC Cl(-)/H(+) antiporter.

Lim, H.H.Stockbridge, R.B.Miller, C.

(2013) Nat Chem Biol 9: 721-725

  • DOI: 10.1038/nchembio.1336
  • Primary Citation of Related Structures:  
    4KJP, 4KJQ, 4KKL, 4KKA, 4KKB, 4KKC, 4KK5, 4KK6, 4KJW, 4KK8

  • PubMed Abstract: 
  • Cl(-)/H(+) antiporters of the CLC superfamily transport anions across biological membranes in varied physiological contexts. These proteins are weakly selective among anions commonly studied, including Cl(-), Br(-), I(-), NO3(-) and SCN(-), but they ...

    Cl(-)/H(+) antiporters of the CLC superfamily transport anions across biological membranes in varied physiological contexts. These proteins are weakly selective among anions commonly studied, including Cl(-), Br(-), I(-), NO3(-) and SCN(-), but they seem to be very selective against F(-). The recent discovery of a new CLC clade of F(-)/H(+) antiporters, which are highly selective for F(-) over Cl(-), led us to investigate the mechanism of Cl(-)-over-F(-) selectivity by a CLC Cl(-)/H(+) antiporter, CLC-ec1. By subjecting purified CLC-ec1 to anion transport measurements, electrophysiological recording, equilibrium ligand-binding studies and X-ray crystallography, we show that F(-) binds in the Cl(-) transport pathway with affinity similar to Cl(-) but stalls the transport cycle. Examination of various mutant antiporters implies a 'lock-down' mechanism of F(-) inhibition, in which F(-), by virtue of its unique hydrogen-bonding chemistry, greatly retards a proton-linked conformational change essential for the transport cycle of CLC-ec1.


    Organizational Affiliation

    1] Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA. [2] Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA. [3].



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H(+)/Cl(-) exchange transporter ClcAAB446Escherichia coli K-12Mutation(s): 0 
Gene Names: b0155clcAeriCJW5012yadQ
Find proteins for P37019 (Escherichia coli (strain K12))
Explore P37019 
Go to UniProtKB:  P37019
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab, heavy chainCE222Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab, light chainDF211Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F
Query on F

Download CCD File 
A, B
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.312α = 90
b = 100.15β = 132.02
c = 169.969γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-05-03 
  • Released Date: 2013-08-21 
  • Deposition Author(s): Lim, H.-H., Miller, C.

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary