6K5F | pdb_00006k5f

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

• PDB DOI: https://doi.org/10.2210/pdb6K5F/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2019-05-28 Released: 2019-08-28 
• Deposition Author(s): Park, K., Lim, H.H.
• Funding Organization(s): Ministry of Science, ICT and Future Planning

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.300 (Depositor), 0.316 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

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

• PubMed: 31409705 
• DOI: https://doi.org/10.1073/pnas.1901822116
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Structure and Function of Neural Network, Korea Brain Research Institute, 41068 Daegu, Republic of Korea.
Department of Structure and Function of Neural Network, Korea Brain Research Institute, 41068 Daegu, Republic of Korea; [e-mail].
Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science & Technology, 42988 Daegu, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B2C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 194.92 kDa 
• Atom Count: 13,247 
• Modeled Residue Count: 1,751 
• Deposited Residue Count: 1,812 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(+)/Cl(-) exchange transporter ClcA	A, B	473	Escherichia coli	Mutation(s): 0  Gene Names:  yadQ, clcA, eriC, A6592_03060, A9819_00720, A9R57_04335, AC067_04570, AC789_1c01550, ACN002_0160, ACN81_28610, ACU57_18640, AM270_18100, AM446_22830, AMK83_01920, AWP75_13405, B1K96_13065, B7C53_01430, B9M99_16180, BANRA_02286, BANRA_02303, BANRA_03326, BB545_20825, BE963_14760, BER14_07860, BFD29_18565, BHF46_07945, BHS81_00575, BHS87_00725, BIQ87_00715, BIU72_13480, BJJ90_21425, BK292_13605, BK373_09530, BK383_20300, BMT53_09575, BMT91_01430, BN17_45791, BVL39_02260, BXT93_20950, BZL31_15015, BZL69_20275, C2M16_10720, C2U48_09685, C3444_11105, C3449_15895, C4J69_03510, C5715_17420, C5P01_08850, C5P43_19885, C7235_20305, C7B02_09235, CG691_14570, CIJ94_20900, COD46_06560, CR538_20715, CRD98_15250, CRM83_15165, CRT46_00820, CV83915_01419, CWM24_04960, CWS33_09545, CXB56_23210, D2184_08665, D2185_20055, D2188_12715, D3821_06135, D3822_17405, D3I61_01530, D3O91_03110, D3Y67_10980, D5618_10265, D5653_16505, D8K42_10345, D9D20_18555, D9D29_16860, D9D31_08820, D9D55_03155, D9D69_06945, D9E22_13175, D9E34_01170, D9F17_00235, D9F57_04830, D9H66_18270, D9H68_13700, D9H94_13970, D9I47_04165, D9I87_01705, D9I88_06500, D9I97_03880, D9J03_00240, D9J11_16750, D9J44_14145, D9J60_02140, DL545_20465, DLW18_08025, DMZ31_06935, DNQ26_06330, DP277_13800, DQF57_05740, DQO13_06325, DS732_05700, DTL43_06000, DTM10_02705, DTM45_12560, DU321_03585, EAI42_18265, EAI44_17040, EAI46_14565, EAI52_10940, EC1094V2_3697, EC3234A_2c01370, Eco118UI_00790, EEP23_00240, EFV01_09785, EFV02_20350, EFV04_15100, EFV08_17265, EFV11_08020, EFV12_18730, EFV14_08750, EFV15_17340, EFV17_09990, EIA10_05995, EL75_3609, EL79_3718, EL80_3665, EOL26_04835, ERS085366_02706, ERS085379_00551, ERS150873_01097, GJ11_00825, HMPREF3040_02596, MJ49_06260, NCTC10082_01396, NCTC10090_02173, NCTC10429_04214, NCTC11126_03619, NCTC12950_04437, NCTC13148_05172, NCTC7922_05796, NCTC7927_04520, NCTC8009_07339, NCTC8179_01364, NCTC8500_04562, NCTC8959_04830, NCTC9036_04037, NCTC9037_04203, NCTC9044_03171, NCTC9050_02039, NCTC9055_00980, NCTC9058_02783, NCTC9062_04200, NCTC9073_03413, NCTC9077_05114, NCTC9111_04278, NCTC9702_04777, NCTC9703_03448, NCTC9706_01351, NCTC9777_00485, PU06_23100, RG28_03970, RK56_028075, RX35_04890, SAMEA3472044_04171, SAMEA3472055_02614, SAMEA3472070_02408, SAMEA3472090_04472, SAMEA3472110_04526, SAMEA3472112_04666, SAMEA3472147_00367, SAMEA3484427_01361, SAMEA3484429_01120, SAMEA3484433_03082, SAMEA3485113_00827, SAMEA3752372_04445, SAMEA3752553_02908, SAMEA3752557_00860, SAMEA3752559_03726, SAMEA3752620_02075, SAMEA3753097_03891, SAMEA3753164_02448, SK85_00155, UC41_07360, UN86_07645, WQ89_09495, WR15_02265, YDC107_3382 Membrane Entity: Yes
UniProt
Find proteins for P37019 (Escherichia coli (strain K12)) Explore P37019  Go to UniProtKB:  P37019

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment, heavy chain	C, E	222	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment, light chain	D, F	211	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	G [auth A], H [auth A], I [auth B], J [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.300 (Depositor), 0.316 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 230.789	α = 90
b = 101.656	β = 132.09
c = 172.003	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Ministry of Science, ICT and Future Planning	Korea, Republic Of	19-BR-01-02
Ministry of Science, ICT and Future Planning	Korea, Republic Of	2017M3C7A 1048086

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2019-09-11
  Changes: Data collection, Database references
• Version 1.2: 2019-11-13
  Changes: Source and taxonomy
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary