4FG6 | pdb_00004fg6

Structure of EcCLC E148A mutant in Glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 
    0.274 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Molecular mechanism of proton transport in CLC Cl-/H+ exchange transporters.

Feng, L.Campbell, E.B.MacKinnon, R.

(2012) Proc Natl Acad Sci U S A 109: 11699-11704

  • DOI: https://doi.org/10.1073/pnas.1205764109
  • Primary Citation Related Structures: 
    4FG6

  • PubMed Abstract: 

    CLC proteins underlie muscle, kidney, bone, and other organ system function by catalyzing the transport of Cl(-) ions across cell and organellar membranes. Some CLC proteins are ion channels while others are pumps that exchange Cl(-) for H(+). The pathway through which Cl(-) ions cross the membrane has been characterized, but the transport of H(+) and the principle by which their movement is coupled to Cl(-) movement is not well understood. Here we show that H(+) transport depends not only on the presence of a specific glutamate residue but also the presence of Cl(-) ions. H(+) transport, however, can be isolated and analyzed in the absence of Cl(-) by mutating the glutamate to alanine and adding carboxylate-containing molecules to solution, consistent with the notion that H(+) transfer is mediated through the entry of a carboxylate group into the anion pathway. Cl(-) ions and carboxylate interact with each other strongly. These data support a mechanism in which the glutamate carboxylate functions as a surrogate Cl(-) ion, but it can accept a H(+) and transfer it between the external solution and the central Cl(-) binding site, coupled to the movement of 2 Cl(-) ions.


  • Organizational Affiliation
    • Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.

Macromolecule Content 

  • Total Structure Weight: 193.02 kDa 
  • Atom Count: 13,158 
  • Modeled Residue Count: 1,749 
  • Deposited Residue Count: 1,796 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H(+)/Cl(-) exchange transporter ClcA
A, B
465Escherichia coli K-12Mutation(s): 0 
Gene Names: b0155clcAeriCJW5012SSON_0167yadQ
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab fragment (Heavy chain)
C, E
222Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab fragment (Light chain)
D, F
211Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free:  0.274 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 221.455α = 90
b = 121.284β = 128.08
c = 151.698γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2013-01-02
    Changes: Database references
  • Version 1.3: 2016-11-09
    Changes: Structure summary
  • Version 1.4: 2017-11-08
    Changes: Refinement description, Source and taxonomy
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2024-11-27
    Changes: Structure summary