6K5F

Crystal structure of the CLC-ec1 deltaNC in presence of 200 mM NaBr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.203 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 116: 17345-17354

  • DOI: 10.1073/pnas.1901822116
  • Primary Citation of Related Structures:  

  • 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 <sup>- </sup> channels and Cl <sup>- </sup>/H <sup>+ </sup> antiporters, have been fu ...

    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 Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science & Technology, 42988 Daegu, Republic of Korea.,Department of Structure and Function of Neural Network, Korea Brain Research Institute, 41068 Daegu, Republic of Korea; hhlim@kbri.re.kr.,Department of Structure and Function of Neural Network, Korea Brain Research Institute, 41068 Daegu, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H(+)/Cl(-) exchange transporter ClcA
A, B
473Escherichia coliMutation(s): 0 
Gene Names: yadQ (clcA, eriC)
Find proteins for J7Q633 (Escherichia coli)
Go to UniProtKB:  J7Q633
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab fragment, heavy chain
C, E
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab fragment, light chain
D, F
211N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download SDF File 
Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.203 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 230.789α = 90.00
b = 101.656β = 132.09
c = 172.003γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-05-28 
  • Released Date: 2019-08-28 
  • Deposition Author(s): Park, K., Lim, H.H.

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 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-11
    Type: Data collection, Database references
  • Version 1.2: 2019-11-13
    Type: Source and taxonomy