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Proton transport, membrane protein PDB id
1f6g
Jmol
Contents
Protein chains
160 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
1f6g
Name: Proton transport, membrane protein
Title: Potassium channel (kcsa) full-length fold
Structure: Voltage-gated potassium channel. Chain: a, b, c, d. Fragment: full-length channel. Engineered: yes. Mutation: yes
Source: Streptomyces lividans. Organism_taxid: 1916. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 8 models
Authors: D.M.Cortes,E.Perozo
Key ref: D.M.Cortes et al. (2001). Molecular architecture of full-length KcsA: role of cytoplasmic domains in ion permeation and activation gating. J Gen Physiol, 117, 165-180. PubMed id: 11158168 Ref: Full text
Date:
21-Jun-00     Release date:   21-Feb-01    
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A334  (KCSA_STRLI) -  Voltage-gated potassium channel
Seq:
Struc: 		160 a.a.
160 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     transport   3 terms 
  Biochemical function     ion channel activity     3 terms  

 

 
    Key reference    
 
 
Full text J Gen Physiol 117:165-180 (2001)
PubMed id: 11158168  
 
 
Molecular architecture of full-length KcsA: role of cytoplasmic domains in ion permeation and activation gating.
D.M.Cortes, L.G.Cuello, E.Perozo.
 
  ABSTRACT  
 
The molecular architecture of the NH(2) and COOH termini of the prokaryotic potassium channel KcsA has been determined using site-directed spin-labeling methods and paramagnetic resonance EPR spectroscopy. Cysteine mutants were generated (residues 5-24 and 121-160) and spin labeled, and the X-band CW EPR spectra were obtained from liposome-reconstituted channels at room temperature. Data on probe mobility (DeltaHo(-1)), accessibility parameters (PiO(2) and PiNiEdda), and inter-subunit spin-spin interaction (Omega) were used as structural constraints to build a three-dimensional folding model of these cytoplasmic domains from a set of simulated annealing and restrained molecular dynamics runs. 32 backbone structures were generated and averaged using fourfold symmetry, and a final mean structure was obtained from the eight lowest energy runs. Based on the present data, together with information from the KcsA crystal structure, a model for the three-dimensional fold of full-length KcsA was constructed. In this model, the NH(2) terminus of KcsA forms an alpha-helix anchored at the membrane-water interface, while the COOH terminus forms a right-handed four-helix bundle that extend some 40-50 A towards the cytoplasm. Functional analysis of COOH-terminal deletion constructs suggest that, while the COOH terminus does not play a substantial role in determining ion permeation properties, it exerts a modulatory role in the pH-dependent gating mechanism.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Synchrotron radiation circular dichroism spectroscopy-defined structure of the C-terminal domain of NaChBac and its role in channel assembly.
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Salt bridges in the miniature viral channel Kcv are important for function.
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Electron spin-echo envelope modulation (ESEEM) reveals water and phosphate interactions with the KcsA potassium channel.
  Biochemistry, 49, 1486-1494.
PDB code: 3ifx
19665988 J.M.Kielec, K.G.Valentine, and A.J.Wand (2010).
A method for solution NMR structural studies of large integral membrane proteins: reverse micelle encapsulation.
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PDB code: 3hpl
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Crystal structure of full-length KcsA in its closed conformation.
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PDB codes: 3efd 3eff
19780836 Z.Yuchi, V.P.Pau, B.X.Lu, M.Junop, and D.S.Yang (2009).
An engineered right-handed coiled coil domain imparts extreme thermostability to the KcsA channel.
  FEBS J, 276, 6236-6246.  
18443286 A.N.Thompson, D.J.Posson, P.V.Parsa, and C.M.Nimigean (2008).
Molecular mechanism of pH sensing in KcsA potassium channels.
  Proc Natl Acad Sci U S A, 105, 6900-6905.  
  18923187 B.Martinac, Y.Saimi, and C.Kung (2008).
Ion channels in microbes.
  Physiol Rev, 88, 1449-1490.  
18488040 C.Ader, R.Schneider, S.Hornig, P.Velisetty, E.M.Wilson, A.Lange, K.Giller, I.Ohmert, M.F.Martin-Eauclaire, D.Trauner, S.Becker, O.Pongs, and M.Baldus (2008).
A structural link between inactivation and block of a K+ channel.
  Nat Struct Mol Biol, 15, 605-612.  
  18797191 J.J.Paynter, P.Sarkies, I.Andres-Enguix, and S.J.Tucker (2008).
Genetic selection of activatory mutations in KcsA.
  Channels (Austin), 2, 413-418.  
  19029373 J.S.Santos, S.M.Grigoriev, and M.Montal (2008).
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18343404 V.Vásquez, M.Sotomayor, D.M.Cortes, B.Roux, K.Schulten, and E.Perozo (2008).
Three-dimensional architecture of membrane-embedded MscS in the closed conformation.
  J Mol Biol, 378, 55-70.  
19016844 Z.Yuchi, V.P.Pau, and D.S.Yang (2008).
GCN4 enhances the stability of the pore domain of potassium channel KcsA.
  FEBS J, 275, 6228-6236.  
17360526 A.Negoda, M.Xian, and R.N.Reusch (2007).
Insight into the selectivity and gating functions of Streptomyces lividans KcsA.
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17415597 C.Boiteux, S.Kraszewski, C.Ramseyer, and C.Girardet (2007).
Ion conductance vs. pore gating and selectivity in KcsA channel: modeling achievements and perspectives.
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17520276 D.E.Logothetis, T.Jin, D.Lupyan, and A.Rosenhouse-Dantsker (2007).
Phosphoinositide-mediated gating of inwardly rectifying K(+) channels.
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Open-state conformation of the KcsA K+ channel: Monte Carlo normal mode following simulations.
  Structure, 15, 1654-1662.  
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Molecular driving forces determining potassium channel slow inactivation.
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Local and global structure of the monomeric subunit of the potassium channel KcsA probed by NMR.
  Biochim Biophys Acta, 1768, 3260-3270.  
17922011 K.A.Baker, C.Tzitzilonis, W.Kwiatkowski, S.Choe, and R.Riek (2007).
Conformational dynamics of the KcsA potassium channel governs gating properties.
  Nat Struct Mol Biol, 14, 1089-1095.  
17541576 M.Baldus (2007).
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  Eur Biophys J, 36, 37-48.  
17657566 M.Baldus (2007).
ICMRBS founder's medal 2006: biological solid-state NMR, methods and applications.
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A quantitative description of KcsA gating I: macroscopic currents.
  J Gen Physiol, 130, 465-478.  
17961504 S.F.Poget, and M.E.Girvin (2007).
Solution NMR of membrane proteins in bilayer mimics: small is beautiful, but sometimes bigger is better.
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16967316 B.Boscolo, E.Laurenti, and E.Ghibaudi (2006).
ESR spectroscopy investigation of the denaturation process of soybean peroxidase induced by guanidine hydrochloride, DMSO or heat.
  Protein J, 25, 379-390.  
16532008 J.F.Cordero-Morales, L.G.Cuello, and E.Perozo (2006).
Voltage-dependent gating at the KcsA selectivity filter.
  Nat Struct Mol Biol, 13, 319-322.  
16532009 J.F.Cordero-Morales, L.G.Cuello, Y.Zhao, V.Jogini, D.M.Cortes, B.Roux, and E.Perozo (2006).
Molecular determinants of gating at the potassium-channel selectivity filter.
  Nat Struct Mol Biol, 13, 311-318.
PDB codes: 1zwi 2atk
16522799 J.H.Chill, J.M.Louis, C.Miller, and A.Bax (2006).
NMR study of the tetrameric KcsA potassium channel in detergent micelles.
  Protein Sci, 15, 684-698.  
17013683 J.H.Chill, J.M.Louis, J.L.Baber, and A.Bax (2006).
Measurement of 15N relaxation in the detergent-solubilized tetrameric KcsA potassium channel.
  J Biomol NMR, 36, 123-136.  
16339887 J.Zimmer, D.A.Doyle, and J.G.Grossmann (2006).
Structural characterization and pH-induced conformational transition of full-length KcsA.
  Biophys J, 90, 1752-1766.  
  17043150 R.Blunck, J.F.Cordero-Morales, L.G.Cuello, E.Perozo, and F.Bezanilla (2006).
Detection of the opening of the bundle crossing in KcsA with fluorescence lifetime spectroscopy reveals the existence of two gates for ion conduction.
  J Gen Physiol, 128, 569-581.  
16272446 S.S.Deol, C.Domene, P.J.Bond, and M.S.Sansom (2006).
Anionic phospholipid interactions with the potassium channel KcsA: simulation studies.
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15869387 B.Roux (2005).
Ion conduction and selectivity in K(+) channels.
  Annu Rev Biophys Biomol Struct, 34, 153-171.  
16301524 L.Gao, X.Mi, V.Paajanen, K.Wang, and Z.Fan (2005).
Activation-coupled inactivation in the bacterial potassium channel KcsA.
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15296727 B.Roux, and K.Schulten (2004).
Computational studies of membrane channels.
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A set of homology models of pore loop domain of six eukaryotic voltage-gated potassium channels Kv1.1-Kv1.6.
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15454428 I.H.Shrivastava, S.R.Durell, and H.R.Guy (2004).
A model of voltage gating developed using the KvAP channel crystal structure.
  Biophys J, 87, 2255-2270.  
  12601086 A.Anishkin, V.Gendel, N.A.Sharifi, C.S.Chiang, L.Shirinian, H.R.Guy, and S.Sukharev (2003).
On the conformation of the COOH-terminal domain of the large mechanosensitive channel MscL.
  J Gen Physiol, 121, 227-244.  
14581184 C.Domene, and M.S.Sansom (2003).
Potassium channel, ions, and water: simulation studies based on the high resolution X-ray structure of KcsA.
  Biophys J, 85, 2787-2800.  
14573870 C.Tian, P.F.Gao, L.H.Pinto, R.A.Lamb, and T.A.Cross (2003).
Initial structural and dynamic characterization of the M2 protein transmembrane and amphipathic helices in lipid bilayers.
  Protein Sci, 12, 2597-2605.  
12533666 J.Li, L.Shi, and A.Karlin (2003).
A photochemical approach to the lipid accessibility of engineered cysteinyl residues.
  Proc Natl Acad Sci U S A, 100, 886-891.  
12524283 S.Ding, and R.Horn (2003).
Effect of S6 tail mutations on charge movement in Shaker potassium channels.
  Biophys J, 84, 295-305.  
12172537 E.Perozo, A.Kloda, D.M.Cortes, and B.Martinac (2002).
Physical principles underlying the transduction of bilayer deformation forces during mechanosensitive channel gating.
  Nat Struct Biol, 9, 696-703.  
12198539 E.Perozo, D.M.Cortes, P.Sompornpisut, A.Kloda, and B.Martinac (2002).
Open channel structure of MscL and the gating mechanism of mechanosensitive channels.
  Nature, 418, 942-948.
PDB codes: 1kyk 1kyl 1kym
12324421 I.M.Williamson, S.J.Alvis, J.M.East, and A.G.Lee (2002).
Interactions of phospholipids with the potassium channel KcsA.
  Biophys J, 83, 2026-2038.  
12189213 J.Li, Q.Xu, D.M.Cortes, E.Perozo, A.Laskey, and A.Karlin (2002).
Reactions of cysteines substituted in the amphipathic N-terminal tail of a bacterial potassium channel with hydrophilic and hydrophobic maleimides.
  Proc Natl Acad Sci U S A, 99, 11605-11610.  
12112695 L.C.Martinez, R.L.Thurmond, P.G.Jones, and G.J.Turner (2002).
Subdomains in the F and G helices of bacteriorhodopsin regulate the conformational transitions of the reprotonation mechanism.
  Proteins, 48, 269-282.  
12124274 N.Bennett, M.Ildefonse, F.Pagès, and M.Ragno (2002).
Gating of heteromeric retinal rod channels by cyclic AMP: role of the C-terminal and pore domains.
  Biophys J, 83, 920-931.  
12324408 P.C.Biggin, and M.S.Sansom (2002).
Open-state models of a potassium channel.
  Biophys J, 83, 1867-1876.  
  11479346 E.Perozo, A.Kloda, D.M.Cortes, and B.Martinac (2001).
Site-directed spin-labeling analysis of reconstituted Mscl in the closed state.
  J Gen Physiol, 118, 193-206.  
11746234 P.Koprowski, and A.Kubalski (2001).
Bacterial ion channels and their eukaryotic homologues.
  Bioessays, 23, 1148-1158.  
11606268 P.Sompornpisut, Y.S.Liu, and E.Perozo (2001).
Calculation of rigid-body conformational changes using restraint-driven Cartesian transformations.
  Biophys J, 81, 2530-2546.  
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 code is shown on the right.