6K5D

Crystal structure of the E148N mutant CLC-ec1 in presence of 200 mM NaBr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H(+)/Cl(-) exchange transporter ClcAA, B473Escherichia coliMutation(s): 1 
Gene Names: 
yadQclcAeriCA6592_03060A9819_00720A9R57_04335AC067_04570AC789_1c01550ACN002_0160ACN81_28610ACU57_18640AM270_18100AM446_22830AMK83_01920AWP75_13405B1K96_13065B7C53_01430B9M99_16180BANRA_02286BANRA_02303BANRA_03326BB545_20825BE963_14760BER14_07860BFD29_18565BHF46_07945BHS81_00575BHS87_00725BIQ87_00715BIU72_13480BJJ90_21425BK292_13605BK373_09530BK383_20300BMT53_09575BMT91_01430BN17_45791BVL39_02260BXT93_20950BZL31_15015BZL69_20275C2M16_10720C2U48_09685C3444_11105C3449_15895C4J69_03510C5715_17420C5P01_08850C5P43_19885C7235_20305C7B02_09235CG691_14570CIJ94_20900COD46_06560CR538_20715CRD98_15250CRM83_15165CRT46_00820CV83915_01419CWM24_04960CWS33_09545CXB56_23210D2184_08665D2185_20055D2188_12715D3821_06135D3822_17405D3I61_01530D3O91_03110D3Y67_10980D5618_10265D5653_16505D8K42_10345D9D20_18555D9D29_16860D9D31_08820D9D55_03155D9D69_06945D9E22_13175D9E34_01170D9F17_00235D9F57_04830D9H66_18270D9H68_13700D9H94_13970D9I47_04165D9I87_01705D9I88_06500D9I97_03880D9J03_00240D9J11_16750D9J44_14145D9J60_02140DL545_20465DLW18_08025DMZ31_06935DNQ26_06330DP277_13800DQF57_05740DQO13_06325DS732_05700DTL43_06000DTM10_02705DTM45_12560DU321_03585EAI42_18265EAI44_17040EAI46_14565EAI52_10940EC1094V2_3697EC3234A_2c01370Eco118UI_00790EEP23_00240EFV01_09785EFV02_20350EFV04_15100EFV08_17265EFV11_08020EFV12_18730EFV14_08750EFV15_17340EFV17_09990EIA10_05995EL75_3609EL79_3718EL80_3665EOL26_04835ERS085366_02706ERS085379_00551ERS150873_01097GJ11_00825HMPREF3040_02596MJ49_06260NCTC10082_01396NCTC10090_02173NCTC10429_04214NCTC11126_03619NCTC12950_04437NCTC13148_05172NCTC7922_05796NCTC7927_04520NCTC8009_07339NCTC8179_01364NCTC8500_04562NCTC8959_04830NCTC9036_04037NCTC9037_04203NCTC9044_03171NCTC9050_02039NCTC9055_00980NCTC9058_02783NCTC9062_04200NCTC9073_03413NCTC9077_05114NCTC9111_04278NCTC9702_04777NCTC9703_03448NCTC9706_01351NCTC9777_00485PU06_23100RG28_03970RK56_028075RX35_04890SAMEA3472044_04171SAMEA3472055_02614SAMEA3472070_02408SAMEA3472090_04472SAMEA3472110_04526SAMEA3472112_04666SAMEA3472147_00367SAMEA3484427_01361SAMEA3484429_01120SAMEA3484433_03082SAMEA3485113_00827SAMEA3752372_04445SAMEA3752553_02908SAMEA3752557_00860SAMEA3752559_03726SAMEA3752620_02075SAMEA3753097_03891SAMEA3753164_02448SK85_00155UC41_07360UN86_07645WQ89_09495WR15_02265YDC107_3382

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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab fragment, heavy chainC, E222Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab fragment, light chainD, F211Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.719α = 90
b = 99.324β = 131.92
c = 171.465γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




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  (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