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PDBsum entry 3kvt

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protein metals links
Potassium channel PDB id
3kvt
Jmol
Contents
Protein chain
103 a.a. *
Metals
_ZN
Waters ×67
* Residue conservation analysis
PDB id:
3kvt
Name: Potassium channel
Title: Tetramerization domain from akv3.1 (shaw-subfamily) voltage- potassium channel
Structure: Potassium channel protein shaw. Chain: a. Fragment: tetramerization (t1) domain. Engineered: yes. Mutation: yes. Other_details: one zn2+ per monomer tetrahedrally coordinat monomer-monomer interface
Source: Aplysia californica. California sea hare. Organism_taxid: 6500. Cell_line: bl21 plys s. Tissue: nerve. Cellular_location: membrane. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21 plys s.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.00Å     R-factor:   0.225     R-free:   0.238
Authors: K.A.Bixby,M.H.Nanao,N.V.Shen,A.Kreusch,H.Bellamy,P.J.Pfaffin S.Choe
Key ref:
K.A.Bixby et al. (1999). Zn2+-binding and molecular determinants of tetramerization in voltage-gated K+ channels. Nat Struct Biol, 6, 38-43. PubMed id: 9886290 DOI: 10.1038/4911
Date:
25-Sep-98     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O76457  (O76457_APLCA) -  Shaw potassium channel Kv3.1a
Seq:
Struc:
514 a.a.
103 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     voltage-gated potassium channel complex   1 term 
  Biological process     protein homooligomerization   2 terms 
  Biochemical function     voltage-gated potassium channel activity     1 term  

 

 
DOI no: 10.1038/4911 Nat Struct Biol 6:38-43 (1999)
PubMed id: 9886290  
 
 
Zn2+-binding and molecular determinants of tetramerization in voltage-gated K+ channels.
K.A.Bixby, M.H.Nanao, N.V.Shen, A.Kreusch, H.Bellamy, P.J.Pfaffinger, S.Choe.
 
  ABSTRACT  
 
The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated K+ channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. Crystal structures of T1 tetramers from Shaw and Shaker subfamilies reveal a common four-layered scaffolding. Within layer 4, on the hypothetical membrane-facing side of the tetramer, the Shaw T1 tetramer contains four zinc ions; each is coordinated by a histidine and two cysteines from one monomer and by one cysteine from an adjacent monomer. The amino acids involved in coordinating the Zn2+ ion occur in a HX5CX20CC sequence motif that is highly conserved among all Shab, Shaw and Shal subfamily members, but is not found in Shaker subfamily members. We demonstrate by coimmunoprecipitation that a few characteristic residues in the subunit interface are crucial for subfamily-specific tetramerization of the T1 domains.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. a, The Shaw T1 tetramer drawn in MOLSCRIPT^37 and rendered using POVRAY version 3.0. The subunit to the front is not shown for clarity. The four-fold axis is vertical down the central cavity. Layer 1 (residues 10−56) is colored in green; layer 2 (residues 57−71) in blue; layer 3 (residues 72−94) in red; and layer 4 (95−111) in yellow. Zinc atoms are shown as gray spheres. b, Stereodiagram of C traces of the superposition of the Shaw T1 (green) and Shaker T1 (magenta) structures (SETOR^ 38) in the same view as in Fig. 1a. Secondary structure elements, N- and C- termini are labeled. Arrows 1 and 2 denote two major variable regions between the two structures. The vertical line represents the four-fold axis. c, Stereodiagram of C traces of the Shaw T1 (green) and Shaker T1 (magenta) to highlight the difference in layer 4, viewed from the top of the teteramer in a direction ~45^o tilted from the four-fold axis. The vertical line in the background represents the four-fold axis.
Figure 2.
Figure 2. a, The zinc binding in the Shaw T1 tetramer. His 75 (layer 3) is shown in red, Cys 102 and Cys 103 are shown in yellow (layer 4). Cys 81 from the adjacent monomer layer 3, is shown in black. Distances between Zn^2+ and coordinating atoms are given.
b, X-ray fluorescence spectra were obtained from single Shaw T1 crystals scanned from 9,200−9,800 eV ( E = 0.8 eV) with a scintillation counter oriented at right angles to the beam (BL1-5, Stanford Synchrotron Radiation Laboratory). The fluorescence intensity was normalized to the flux of the incident X-ray as measured by an ion chamber. The data were processed with the program DISCO^39. The values of f" come from fitting the data to the theoretical absorption curve for Zn in the regions above and below the Zn K edge. The theoretical value for the K edge of elemental Zn is 9,659 eV; the observed value for two separate measurements was found to be about 2 eV higher. Spectra taken on crystallization buffer and loop, cryoprotectant and loop, and loop alone did not demonstrate any observable signal for identical scans (data not shown). X-ray fluorescence scanning of crystals at wavelengths around the Mn^2+ and Co^2+ K edges also did not show any signal. Shaw T1 anomalous dispersion data set was collected at 9,670 eV (1.28 Å). Overall completeness was 99.9%, and Bijvoet pairs were 67% complete to 1.95 Å. An 8 peak was located in an anomalous difference Patterson map which corresponded to the site of the zinc in the monomer. c, Stereodiagram of (2F[ o] - F[c]) electron density maps of Shaw T1 superimposed with the final refined model for the region near the layer 4 in a viewpoint similar to that in (a). Maps are contoured at 1 . d, Stereodiagram of (2F[o] - []F[c]) electron density maps of Shaker T1 superimposed with the final refined model for the region showing the layers 3 and 4 in the region near the C-terminus of layer 4. Maps are contoured at 1 .
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 38-43) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20018952 E.D.Burg, O.Platoshyn, I.F.Tsigelny, B.Lozano-Ruiz, B.K.Rana, and J.X.Yuan (2010).
Tetramerization domain mutations in KCNA5 affect channel kinetics and cause abnormal trafficking patterns.
  Am J Physiol Cell Physiol, 298, C496-C509.  
20137774 H.Odeh, K.L.Hunker, I.A.Belyantseva, H.Azaiez, M.R.Avenarius, L.Zheng, L.M.Peters, L.H.Gagnon, N.Hagiwara, M.J.Skynner, M.H.Brilliant, N.D.Allen, S.Riazuddin, K.R.Johnson, Y.Raphael, H.Najmabadi, T.B.Friedman, J.R.Bartles, R.J.Smith, and D.C.Kohrman (2010).
Mutations in Grxcr1 are the basis for inner ear dysfunction in the pirouette mouse.
  Am J Hum Genet, 86, 148-160.  
20037152 S.Hou, L.E.Vigeland, G.Zhang, R.Xu, M.Li, S.H.Heinemann, and T.Hoshi (2010).
Zn2+ activates large conductance Ca2+-activated K+ channel via an intracellular domain.
  J Biol Chem, 285, 6434-6442.  
19624124 A.M.Davis, and J.M.Berg (2009).
Homodimerization and heterodimerization of minimal zinc(II)-binding-domain peptides of T-cell proteins CD4, CD8alpha, and Lck.
  J Am Chem Soc, 131, 11492-11497.  
18836841 A.V.Pischalnikova, and O.S.Sokolova (2009).
The domain and conformational organization in potassium voltage-gated ion channels.
  J Neuroimmune Pharmacol, 4, 71-82.  
19717558 E.Bocksteins, A.J.Labro, E.Mayeur, T.Bruyns, J.P.Timmermans, D.Adriaensen, and D.J.Snyders (2009).
Conserved negative charges in the N-terminal tetramerization domain mediate efficient assembly of Kv2.1 and Kv2.1/Kv6.4 channels.
  J Biol Chem, 284, 31625-31634.  
19361449 I.S.Dementieva, V.Tereshko, Z.A.McCrossan, E.Solomaha, D.Araki, C.Xu, N.Grigorieff, and S.A.Goldstein (2009).
Pentameric assembly of potassium channel tetramerization domain-containing protein 5.
  J Mol Biol, 387, 175-191.
PDB codes: 3drx 3dry 3drz
19185023 M.Harvey, J.Karolat, Y.Sakai, and B.Sokolowski (2009).
PPTX, a pentraxin domain-containing protein, interacts with the T1 domain of K v 4.
  J Neurosci Res, 87, 1841-1847.  
19074135 M.Mederos Y Schnitzler, S.Rinné, L.Skrobek, V.Renigunta, G.Schlichthörl, C.Derst, T.Gudermann, J.Daut, and R.Preisig-Müller (2009).
Mutation of histidine 105 in the t1 domain of the potassium channel kv2.1 disrupts heteromerization with kv6.3 and kv6.4.
  J Biol Chem, 284, 4695-4704.  
17890387 C.Picco, A.Naso, P.Soliani, and F.Gambale (2008).
The zinc binding site of the Shaker channel KDC1 from Daucus carota.
  Biophys J, 94, 424-433.  
18042678 J.C.Ebert, and R.B.Altman (2008).
Robust recognition of zinc binding sites in proteins.
  Protein Sci, 17, 54-65.  
18415675 K.Wang (2008).
Modulation by clamping: Kv4 and KChIP interactions.
  Neurochem Res, 33, 1964-1969.  
18357523 M.Covarrubias, A.Bhattacharji, J.A.De Santiago-Castillo, K.Dougherty, Y.A.Kaulin, T.R.Na-Phuket, and G.Wang (2008).
The neuronal Kv4 channel complex.
  Neurochem Res, 33, 1558-1567.  
18165683 R.Wiener, Y.Haitin, L.Shamgar, M.C.Fernández-Alonso, A.Martos, O.Chomsky-Hecht, G.Rivas, B.Attali, and J.A.Hirsch (2008).
The KCNQ1 (Kv7.1) COOH terminus, a multitiered scaffold for subunit assembly and protein interaction.
  J Biol Chem, 283, 5815-5830.
PDB code: 3bj4
18782578 Y.Fujiwara, and D.L.Minor (2008).
X-ray crystal structure of a TRPM assembly domain reveals an antiparallel four-stranded coiled-coil.
  J Mol Biol, 383, 854-870.
PDB code: 3e7k
17331952 G.Wang, C.Strang, P.J.Pfaffinger, and M.Covarrubias (2007).
Zn2+-dependent redox switch in the intracellular T1-T1 interface of a Kv channel.
  J Biol Chem, 282, 13637-13647.  
17541769 I.S.Gabashvili, B.H.Sokolowski, C.C.Morton, and A.B.Giersch (2007).
Ion channel gene expression in the inner ear.
  J Assoc Res Otolaryngol, 8, 305-328.  
17329207 R.J.Howard, K.A.Clark, J.M.Holton, and D.L.Minor (2007).
Structural insight into KCNQ (Kv7) channel assembly and channelopathy.
  Neuron, 53, 663-675.
PDB code: 2ovc
17473864 Y.Tsumura, A.Matsumoto, N.Tani, T.Ujino-Ihara, T.Kado, H.Iwata, and K.Uchida (2007).
Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implications for management and conservation.
  Heredity, 99, 161-172.  
16515810 A.R.Kay (2006).
Imaging synaptic zinc: promises and perils.
  Trends Neurosci, 29, 200-206.  
  16533897 G.Wang, and M.Covarrubias (2006).
Voltage-dependent gating rearrangements in the intracellular T1-T1 interface of a K+ channel.
  J Gen Physiol, 127, 391-400.  
16725367 P.Pouliquin, S.M.Pace, S.M.Curtis, P.J.Harvey, E.M.Gallant, F.Zorzato, M.G.Casarotto, and A.F.Dulhunty (2006).
Effects of an alpha-helical ryanodine receptor C-terminal tail peptide on ryanodine receptor activity: modulation by Homer.
  Int J Biochem Cell Biol, 38, 1700-1715.  
16846855 P.R.Tsuruda, D.Julius, and D.L.Minor (2006).
Coiled coils direct assembly of a cold-activated TRP channel.
  Neuron, 51, 201-212.  
  16801386 R.K.Finol-Urdaneta, N.Strüver, and H.Terlau (2006).
Molecular and Functional Differences between Heart mKv1.7 Channel Isoforms.
  J Gen Physiol, 128, 133-145.  
16111489 B.Li, and W.J.Gallin (2005).
Computational identification of residues that modulate voltage sensitivity of voltage-gated potassium channels.
  BMC Struct Biol, 5, 16.  
  15955876 G.Wang, M.Shahidullah, C.A.Rocha, C.Strang, P.J.Pfaffinger, and M.Covarrubias (2005).
Functionally active t1-t1 interfaces revealed by the accessibility of intracellular thiolate groups in kv4 channels.
  J Gen Physiol, 126, 55-69.  
15664174 J.M.Robinson, and C.Deutsch (2005).
Coupled tertiary folding and oligomerization of the T1 domain of Kv channels.
  Neuron, 45, 223-232.  
16161108 M.R.Salaman, and J.Warwicker (2005).
Anomalies in the ionic properties of serum albumin.
  Proteins, 61, 468-472.  
16207353 P.J.Stogios, G.S.Downs, J.J.Jauhal, S.K.Nandra, and G.G.Privé (2005).
Sequence and structural analysis of BTB domain proteins.
  Genome Biol, 6, R82.  
15473968 A.Kosolapov, L.Tu, J.Wang, and C.Deutsch (2004).
Structure acquisition of the T1 domain of Kv1.3 during biogenesis.
  Neuron, 44, 295-307.  
15357420 B.L.Resendes, S.F.Kuo, N.G.Robertson, A.B.Giersch, D.Honrubia, O.Ohara, J.C.Adams, and C.C.Morton (2004).
Isolation from cochlea of a novel human intronless gene with predominant fetal expression.
  J Assoc Res Otolaryngol, 5, 185-202.  
15313238 J.M.Gulbis, and D.A.Doyle (2004).
Potassium channel structures: do they conform?
  Curr Opin Struct Biol, 14, 440-446.  
15489237 Q.Chang, E.Gyftogianni, S.F.van de Graaf, S.Hoefs, F.A.Weidema, R.J.Bindels, and J.G.Hoenderop (2004).
Molecular determinants in TRPV5 channel assembly.
  J Biol Chem, 279, 54304-54311.  
14980207 R.H.Scannevin, K.Wang, F.Jow, J.Megules, D.C.Kopsco, W.Edris, K.C.Carroll, Q.Lü, W.Xu, Z.Xu, A.H.Katz, S.Olland, L.Lin, M.Taylor, M.Stahl, K.Malakian, W.Somers, L.Mosyak, M.R.Bowlby, P.Chanda, and K.J.Rhodes (2004).
Two N-terminal domains of Kv4 K(+) channels regulate binding to and modulation by KChIP1.
  Neuron, 41, 587-598.
PDB codes: 1s1e 1s1g
12754210 C.Strang, K.Kunjilwar, D.DeRubeis, D.Peterson, and P.J.Pfaffinger (2003).
The role of Zn2+ in Shal voltage-gated potassium channel formation.
  J Biol Chem, 278, 31361-31371.  
12642579 D.Kerschensteiner, F.Monje, and M.Stocker (2003).
Structural determinants of the regulation of the voltage-gated potassium channel Kv2.1 by the modulatory alpha-subunit Kv9.3.
  J Biol Chem, 278, 18154-18161.  
12835418 M.H.Nanao, W.Zhou, P.J.Pfaffinger, and S.Choe (2003).
Determining the basis of channel-tetramerization specificity by x-ray crystallography and a sequence-comparison algorithm: Family Values (FamVal).
  Proc Natl Acad Sci U S A, 100, 8670-8675.
PDB code: 1nn7
12560340 M.Ju, L.Stevens, E.Leadbitter, and D.Wray (2003).
The Roles of N- and C-terminal determinants in the activation of the Kv2.1 potassium channel.
  J Biol Chem, 278, 12769-12778.  
13678422 S.Prag, and J.C.Adams (2003).
Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.
  BMC Bioinformatics, 4, 42.  
11826262 C.Deutsch (2002).
Potassium channel ontogeny.
  Annu Rev Physiol, 64, 19-46.  
12021261 H.T.Kurata, G.S.Soon, J.R.Eldstrom, G.W.Lu, D.F.Steele, and D.Fedida (2002).
Amino-terminal determinants of U-type inactivation of voltage-gated K+ channels.
  J Biol Chem, 277, 29045-29053.  
12062021 J.J.Rosenthal, and F.Bezanilla (2002).
Extensive editing of mRNAs for the squid delayed rectifier K+ channel regulates subunit tetramerization.
  Neuron, 34, 743-757.  
12032359 R.Preisig-Müller, G.Schlichthörl, T.Goerge, S.Heinen, A.Brüggemann, S.Rajan, C.Derst, R.W.Veh, and J.Daut (2002).
Heteromerization of Kir2.x potassium channels contributes to the phenotype of Andersen's syndrome.
  Proc Natl Acad Sci U S A, 99, 7774-7779.  
11572962 B.A.Yi, D.L.Minor, Y.F.Lin, Y.N.Jan, and L.Y.Jan (2001).
Controlling potassium channel activities: Interplay between the membrane and intracellular factors.
  Proc Natl Acad Sci U S A, 98, 11016-11023.  
11604135 J.C.Quirk, and P.H.Reinhart (2001).
Identification of a novel tetramerization domain in large conductance K(ca) channels.
  Neuron, 32, 13-23.  
11286888 O.Sokolova, L.Kolmakova-Partensky, and N.Grigorieff (2001).
Three-dimensional structure of a voltage-gated potassium channel at 2.5 nm resolution.
  Structure, 9, 215-220.  
10733968 B.K.Berdiev, V.G.Shlyonsky, K.H.Karlson, B.A.Stanton, and I.I.Ismailov (2000).
Gating of amiloride-sensitive Na(+) channels: subunit-subunit interactions and inhibition by the cystic fibrosis transmembrane conductance regulator.
  Biophys J, 78, 1881-1894.  
10866950 C.G.Viloria, F.Barros, T.Giráldez, D.Gómez-Varela, and P.de la Peña (2000).
Differential effects of amino-terminal distal and proximal domains in the regulation of human erg K(+) channel gating.
  Biophys J, 79, 231-246.  
11007484 D.L.Minor, Y.F.Lin, B.C.Mobley, A.Avelar, Y.N.Jan, L.Y.Jan, and J.M.Berger (2000).
The polar T1 interface is linked to conformational changes that open the voltage-gated potassium channel.
  Cell, 102, 657-670.
PDB codes: 1dsx 1qdv 1qdw
10651649 L.Tu, J.Wang, A.Helm, W.R.Skach, and C.Deutsch (2000).
Transmembrane biogenesis of Kv1.3.
  Biochemistry, 39, 824-836.  
10716722 N.Zerangue, Y.N.Jan, and L.Y.Jan (2000).
An artificial tetramerization domain restores efficient assembly of functional Shaker channels lacking T1.
  Proc Natl Acad Sci U S A, 97, 3591-3595.  
10981635 P.C.Biggin, T.Roosild, and S.Choe (2000).
Potassium channel structure: domain by domain.
  Curr Opin Struct Biol, 10, 456-461.  
10956024 W.R.Kobertz, C.Williams, and C.Miller (2000).
Hanging gondola structure of the T1 domain in a voltage-gated K(+) channel.
  Biochemistry, 39, 10347-10352.  
10753881 X.Yao, W.Liu, S.Tian, H.Rafi, A.S.Segal, and G.V.Desir (2000).
Close association of the N terminus of Kv1.3 with the pore region.
  J Biol Chem, 275, 10859-10863.  
10402187 D.M.Papazian (1999).
Potassium channels: some assembly required.
  Neuron, 23, 7.  
10395571 G.Yellen (1999).
The bacterial K+ channel structure and its implications for neuronal channels.
  Curr Opin Neurobiol, 9, 267-273.  
10530995 M.S.Sansom (1999).
Putting the parts together.
  Curr Biol, 9, R738-R741.  
10470033 S.Choe, A.Kreusch, and P.J.Pfaffinger (1999).
Towards the three-dimensional structure of voltage-gated potassium channels.
  Trends Biochem Sci, 24, 345-349.  
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.