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PDBsum entry 2d4z
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protein Protein-protein interface(s) links
Transport protein PDB id
2d4z

 

 

 

 

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Contents
Protein chains
169 a.a. *
171 a.a. *
* Residue conservation analysis
PDB id:
2d4z
Name: Transport protein
Title: Crystal structure of the cytoplasmic domain of the chloride channel clc-0
Structure: Chloride channel protein. Chain: a, b. Fragment: clc-0 cytoplasmic domain. Engineered: yes
Source: Torpedo marmorata. Marbled electric ray. Organism_taxid: 7788. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PQS)
Resolution:
3.10Å     R-factor:   0.274     R-free:   0.309
Authors: R.Dutzler,S.Meyer
Key ref:
S.Meyer and R.Dutzler (2006). Crystal Structure of the Cytoplasmic Domain of the Chloride Channel ClC-0. Structure, 14, 299-307. PubMed id: 16472749 DOI: 10.1016/j.str.2005.10.008
Date:
26-Oct-05     Release date:   14-Feb-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21564  (CICH_TORMA) -  Chloride channel protein from Torpedo marmorata
Seq:
Struc: 		 
Seq:
Struc: 		805 a.a.
169 a.a.
Protein chain
Pfam   ArchSchema ?
P21564  (CICH_TORMA) -  Chloride channel protein from Torpedo marmorata
Seq:
Struc: 		 
Seq:
Struc: 		805 a.a.
171 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.str.2005.10.008 Structure 14:299-307 (2006)
PubMed id: 16472749  
 
 
Crystal Structure of the Cytoplasmic Domain of the Chloride Channel ClC-0.
S.Meyer, R.Dutzler.
 
  ABSTRACT  
 
Ion channels are frequently organized in a modular fashion and consist of a membrane-embedded pore domain and a soluble regulatory domain. A similar organization is found for the ClC family of Cl(-) channels and transporters. Here, we describe the crystal structure of the cytoplasmic domain of ClC-0, the voltage-dependent Cl(-) channel from T. marmorata. The structure contains a folded core of two tightly interacting cystathionine beta-synthetase (CBS) subdomains. The two subdomains are connected by a 96 residue mobile linker that is disordered in the crystals. As revealed by analytical ultracentrifugation, the domains form dimers, thereby most likely extending the 2-fold symmetry of the transmembrane pore. The structure provides insight into the organization of the cytoplasmic domains within the ClC family and establishes a framework for guiding future investigations on regulatory mechanisms.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Topology and Structure of the ClC-0 Domain
(A) Stereoview of a C-a trace of the ClC-0 domain. Selected residues are labeled according to their position in the ClC-0 sequence.
(B) Cartoon of the secondary structure. The two CBS subdomains are colored in blue and red, respectively, additional ordered parts of the structure are shown in gray, and disordered regions are marked by dashed lines. The residue numbers (ClC-0) at the beginning and end of the secondary structure elements are shown.
(C) Ribbon representation of the ClC-0 domain in two orientations. Colors are according to (A). The relationship between the two views is indicated. This figure and Figure 4 were prepared with DINO (http://www.dino3d.org).
(D) Propensity of the ClC-0 domain sequence to form an ordered structure. P(d) describes the propensity for disorder; residues with values above P(d) = 0.5 are likely to be unstructured. The segments corresponding to the subdomains are labeled.
 
  The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 299-307) copyright 2006.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21527911 L.Leisle, C.F.Ludwig, F.A.Wagner, T.J.Jentsch, and T.Stauber (2011).
ClC-7 is a slowly voltage-gated 2Cl(-)/1H(+)-exchanger and requires Ostm1 for transport activity.
  EMBO J, 30, 2140-2152.  
19827947 C.Duran, C.H.Thompson, Q.Xiao, and H.C.Hartzell (2010).
Chloride channels: often enigmatic, rarely predictable.
  Annu Rev Physiol, 72, 95.  
20049483 L.Wellhauser, C.D'Antonio, and C.E.Bear (2010).
ClC transporters: discoveries and challenges in defining the mechanisms underlying function and regulation of ClC-5.
  Pflugers Arch, 460, 543-557.  
20822503 M.Jossier, L.Kroniewicz, F.Dalmas, D.Le Thiec, G.Ephritikhine, S.Thomine, H.Barbier-Brygoo, A.Vavasseur, S.Filleur, and N.Leonhardt (2010).
The Arabidopsis vacuolar anion transporter, AtCLCc, is involved in the regulation of stomatal movements and contributes to salt tolerance.
  Plant J, 64, 563-576.  
19636075 A.De Angeli, O.Moran, S.Wege, S.Filleur, G.Ephritikhine, S.Thomine, H.Barbier-Brygoo, and F.Gambale (2009).
ATP binding to the C terminus of the Arabidopsis thaliana nitrate/proton antiporter, AtCLCa, regulates nitrate transport into plant vacuoles.
  J Biol Chem, 284, 26526-26532.  
19574231 C.H.Thompson, P.R.Olivetti, M.D.Fuller, C.S.Freeman, D.McMaster, R.J.French, J.Pohl, J.Kubanek, and N.A.McCarty (2009).
Isolation and characterization of a high affinity peptide inhibitor of ClC-2 chloride channels.
  J Biol Chem, 284, 26051-26062.  
19713962 G.Zifarelli, and M.Pusch (2009).
Intracellular regulation of human ClC-5 by adenine nucleotides.
  EMBO Rep, 10, 1111-1116.  
19711355 I.Cornejo, M.I.Niemeyer, L.Zúñiga, Y.R.Yusef, F.V.Sepúlveda, and L.P.Cid (2009).
Rapid recycling of ClC-2 chloride channels between plasma membrane and endosomes: role of a tyrosine endocytosis motif in surface retrieval.
  J Cell Physiol, 221, 650-657.  
19135547 L.Ma, G.Y.Rychkov, and A.H.Bretag (2009).
Functional study of cytoplasmic loops of human skeletal muscle chloride channel, hClC-1.
  Int J Biochem Cell Biol, 41, 1402-1409.  
18853181 V.Plans, G.Rickheit, and T.J.Jentsch (2009).
Physiological roles of CLC Cl(-)/H (+) exchangers in renal proximal tubules.
  Pflugers Arch, 458, 23-37.  
  18227270 A.Accardi (2008).
To ATP or Not To ATP: This Is the Question.
  J Gen Physiol, 131, 105-108.  
18648499 G.Q.Martinez, and M.Maduke (2008).
A cytoplasmic domain mutation in ClC-Kb affects long-distance communication across the membrane.
  PLoS ONE, 3, e2746.  
  18227271 G.Zifarelli, and M.Pusch (2008).
The Muscle Chloride Channel ClC-1 Is Not Directly Regulated by Intracellular ATP.
  J Gen Physiol, 131, 109-116.  
  18931440 M.Lucas, D.Kortazar, E.Astigarraga, J.A.Fernández, J.M.Mato, M.L.Martínez-Chantar, and L.A.Martínez-Cruz (2008).
Purification, crystallization and preliminary X-ray diffraction analysis of the CBS-domain pair from the Methanococcus jannaschii protein MJ0100.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 936-941.  
18021800 M.Proudfoot, S.A.Sanders, A.Singer, R.Zhang, G.Brown, A.Binkowski, L.Xu, J.A.Lukin, A.G.Murzin, A.Joachimiak, C.H.Arrowsmith, A.M.Edwards, A.V.Savchenko, and A.F.Yakunin (2008).
Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain.
  J Mol Biol, 375, 301-315.
PDB codes: 1pvm 2qh1
  18824589 X.D.Zhang, P.Y.Tseng, and T.Y.Chen (2008).
ATP inhibition of CLC-1 is controlled by oxidation and reduction.
  J Gen Physiol, 132, 421-428.  
17693413 B.Bennetts, M.W.Parker, and B.A.Cromer (2007).
Inhibition of skeletal muscle ClC-1 chloride channels by low intracellular pH and ATP.
  J Biol Chem, 282, 32780-32791.  
17452784 P.Day, A.Sharff, L.Parra, A.Cleasby, M.Williams, S.Hörer, H.Nar, N.Redemann, I.Tickle, and J.Yon (2007).
Structure of a CBS-domain pair from the regulatory gamma1 subunit of human AMPK in complex with AMP and ZMP.
  Acta Crystallogr D Biol Crystallogr, 63, 587-596.
PDB codes: 2uv4 2uv5 2uv6 2uv7
  17664348 P.Y.Tseng, B.Bennetts, and T.Y.Chen (2007).
Cytoplasmic ATP inhibition of CLC-1 is enhanced by low pH.
  J Gen Physiol, 130, 217-221.  
17289942 R.Townley, and L.Shapiro (2007).
Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase.
  Science, 315, 1726-1729.
PDB codes: 2oox 2ooy
17562318 S.Markovic, and R.Dutzler (2007).
The structure of the cytoplasmic domain of the chloride channel ClC-Ka reveals a conserved interaction interface.
  Structure, 15, 715-725.
PDB code: 2pfi
17195847 S.Meyer, S.Savaresi, I.C.Forster, and R.Dutzler (2007).
Nucleotide recognition by the cytoplasmic domain of the human chloride transporter ClC-5.
  Nat Struct Mol Biol, 14, 60-67.
PDB codes: 2j9l 2ja3
16554809 C.Miller (2006).
ClC chloride channels viewed through a transporter lens.
  Nature, 440, 484-489.  
17115052 E.A.Bykova, X.D.Zhang, T.Y.Chen, and J.Zheng (2006).
Large movement in the C terminus of CLC-0 chloride channel during slow gating.
  Nat Struct Mol Biol, 13, 1115-1119.  
17042925 E.C.Aromataris, and G.Y.Rychkov (2006).
ClC-1 chloride channel: Matching its properties to a role in skeletal muscle.
  Clin Exp Pharmacol Physiol, 33, 1118-1123.  
16814540 R.Dutzler (2006).
The ClC family of chloride channels and transporters.
  Curr Opin Struct Biol, 16, 439-446.  
16914964 S.Sile, C.G.Vanoye, and A.L.George (2006).
Molecular physiology of renal ClC chloride channels/transporters.
  Curr Opin Nephrol Hypertens, 15, 511-516.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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