6K5I

Crystal structure of the E148D/R147A/F317A mutant CLC-ec1 in the presence of 20 mM NaBr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Mutation of external glutamate residue reveals a new intermediate transport state and anion binding site in a CLC Cl-/H+antiporter.

Park, K.Lee, B.C.Lim, H.H.

(2019) Proc Natl Acad Sci U S A 116: 17345-17354

  • DOI: https://doi.org/10.1073/pnas.1901822116
  • Primary Citation of Related Structures:  
    6AD7, 6AD8, 6ADA, 6ADB, 6ADC, 6K5A, 6K5D, 6K5F, 6K5I

  • PubMed Abstract: 

    The CLC family of proteins are involved in a variety of physiological processes to control cellular chloride concentration. Two distinct classes of CLC proteins, Cl - channels and Cl - /H + antiporters, have been functionally and structurally investigated over the last several decades. Previous studies have suggested that the conformational heterogeneity of the critical glutamate residue, Glu ex , could explain the transport cycle of CLC-type Cl - /H + antiporters. However, the presence of multiple conformations ( Up , Middle , and Down ) of the Glu ex has been suggested from combined structural snapshots of 2 different CLC antiporters: CLC-ec1 from Escherichia coli and cmCLC from a thermophilic red alga, Cyanidioschyzon merolae Thus, we aimed to investigate further the heterogeneity of Glu ex -conformations in CLC-ec1, the most deeply studied CLC antiporter, at both functional and structural levels. Here, we show that the crystal structures of the Glu ex mutant E148D and wild-type CLC-ec1 with varying anion concentrations suggest a structural intermediate, the " Midlow " conformation. We also found that an extra anion can be located above the external Cl - -binding site in the E148D mutant when the anion concentration is high. Moreover, we observed that a carboxylate in solution can occupy either the external or central Cl - -binding site in the ungated E148A mutant using an anomalously detectable short carboxylic acid, bromoacetate. These results lend credibility to the idea that the Glu ex can take at least 3 distinct conformational states during the transport cycle of a single CLC antiporter.


  • Organizational Affiliation

    Department of Structure and Function of Neural Network, Korea Brain Research Institute, 41068 Daegu, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H(+)/Cl(-) exchange transporter ClcA
A, B
473Escherichia coli MS 117-3Mutation(s): 3 
Gene Names: clcAeriCHMPREF9542_03540
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment, heavy chain
C, E
222Mus musculusMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.914α = 90
b = 98.826β = 131.88
c = 170.295γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science, ICT and Future PlanningKorea, Republic Of19-BR-01-02
Ministry of Science, ICT and Future PlanningKorea, Republic Of2017M3C7A 1048086

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary