2H2P

Crystal structure of CLC-ec1 in complex with Fab fragment in SeCN-


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Uncoupling of a CLC Cl(-)/H(+) Exchange Transporter by Polyatomic Anions

Nguitragool, W.Miller, C.

(2006) J Mol Biol 362: 682-690

  • DOI: https://doi.org/10.1016/j.jmb.2006.07.006
  • Primary Citation of Related Structures:  
    2H2P, 2H2S

  • PubMed Abstract: 

    CLC-ec1 is a bacterial archetype of CLC transporters, a ubiquitous class of proteins that catalyze transmembrane exchange of Cl- and H+ necessary for pH regulation of numerous physiological processes. Despite a profusion of high-resolution structures, the molecular mechanism of exchange remains unknown. Here, we rigorously demonstrate strict exchange stoichiometry of 2 Cl-/1 H+. In addition to Cl- and Br-, two non-halide ions, NO3- and SCN-, are shown to be transported by CLC-ec1, but with reduced H+ counter-transport. The loss of proton coupling to these anions is accompanied by an absence of bound anions in the central and external Cl- binding sites in the protein's anion selectivity region, as revealed by crystallographic comparison of Br- and SeCN- bound to this region.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CLC Cl transporter
A, B
465Escherichia coliMutation(s): 0 
Gene Names: clcAeriC
Membrane Entity: Yes 
UniProt
Find proteins for P37019 (Escherichia coli (strain K12))
Explore P37019 
Go to UniProtKB:  P37019
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37019
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FAB fragment, heavy chain
C, E
221Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q4VBH1 (Rattus norvegicus)
Explore Q4VBH1 
Go to UniProtKB:  Q4VBH1
Entity Groups  
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UniProt GroupQ4VBH1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FAB fragment, light chain
D, F
211Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.581α = 90
b = 121.578β = 128.25
c = 151.24γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary