PDBsum entry 1nn7

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protein metals links
Membrane protein PDB id
Protein chain
105 a.a. *
Waters ×57
* Residue conservation analysis
PDB id:
Name: Membrane protein
Title: Crystal structure of the tetramerization domain of the shal gated potassium channel
Structure: Potassium channel kv4.2. Chain: a. Fragment: n-terminal domain (residues 42-146), tetramerizat domain. Synonym: shal voltage-gated potassium channel. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: kcnd2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PDB file)
2.10Å     R-factor:   0.230     R-free:   0.277
Authors: W.Zhou,S.Choe
Key ref:
M.H.Nanao et al. (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. PubMed id: 12835418 DOI: 10.1073/pnas.1432840100
13-Jan-03     Release date:   15-Jul-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q63881  (KCND2_RAT) -  Potassium voltage-gated channel subfamily D member 2
630 a.a.
105 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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: 10.1073/pnas.1432840100 Proc Natl Acad Sci U S A 100:8670-8675 (2003)
PubMed id: 12835418  
Determining the basis of channel-tetramerization specificity by x-ray crystallography and a sequence-comparison algorithm: Family Values (FamVal).
M.H.Nanao, W.Zhou, P.J.Pfaffinger, S.Choe.
We have developed a semiempirical algorithm called Family Values (FamVal), which identifies residues that encode functional specificity in a protein sequence. Given a multiple sequence alignment (MSA) grouped into functionally distinct subfamilies, FamVal calculates a specificity score for each subfamily at every amino acid position of an MSA. This algorithm was used to predict specificity-encoding positions within the tetramerization assembly (T1) domain of voltage-gated potassium (Kv) channel subfamilies Kv3 and Kv4. The importance of one such position (Arg to Ala at MSA position 93) was confirmed by in vitro pull-down assays. The structural basis of this assembly discrimination was elucidated by determining the crystal structure of the Kv4 T1 domain and comparing it to the Kv3 T1 domain.
  Selected figure(s)  
Figure 1.
Fig. 1. Schematic representation of chemical-property vectors. Vectors are constructed for each MSA position independently for a given subfamily and again for the entire family. Here, an example MSA containing six sequences from two subfamilies is plotted in two dimensions (hydrophobicity on the y and polarity on the x axis). Red and blue vectors represent subfamily vectors for subfamilies A and B, respectively. In the leftmost plot, they represent the sums of three Ds for subfamily A, or three Es for subfamily B. A purple vector represents the overall vector at the MSA position. The subfamily's FamVal scores are computed by comparing the distances (green dotted lines) between the subfamily-vector endpoints and the overall-vector endpoints, weighted by multiplying by sin ( /2). A table containing normalized chemical-property scales used for FamVal scores in this study is shown at the bottom.
Figure 4.
Fig. 4. In vitro pull-down assay of purified Kv3 and Kv4 T1 mutants. Below the gels, bait proteins Kv3(WT), Kv3(A63R), and Kv4(WTL) that are tagged by N-terminal 6-histidine tags are shown (Upper). Molecular weights of these bands range from 12 to 15 kDa. To test self-association of Kv4, a Kv4 WT with a 16-aa C-terminal extension [Kv4(WTL)] was used. The difference in size allowed us to distinguish them by SDS/PAGE. (Lower) The test proteins [Kv4(WT) and Kv4(R93A)] that are not histidine-tagged. Black bars represent the presence of those bait and test proteins in the reaction mixtures. The presence of the corresponding bands in the gels indicates the assembly affinity between them.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
19170764 N.Ito, M.Watanabe-Matsui, K.Igarashi, and K.Murayama (2009).
Crystal structure of the Bach1 BTB domain and its regulation of homodimerization.
  Genes Cells, 14, 167-178.  
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.  
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.  
  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.  
16096338 B.Callsen, D.Isbrandt, K.Sauter, L.S.Hartmann, O.Pongs, and R.Bähring (2005).
Contribution of N- and C-terminal Kv4.2 channel domains to KChIP interaction [corrected]
  J Physiol, 568, 397-412.  
  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.  
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.  
15473959 J.S.Trimmer (2004).
Peering into the birth canal during ion channel parturition.
  Neuron, 44, 214-216.  
14980206 W.Zhou, Y.Qian, K.Kunjilwar, P.J.Pfaffinger, and S.Choe (2004).
Structural insights into the functional interaction of KChIP1 with Shal-type K(+) channels.
  Neuron, 41, 573-586.
PDB code: 1s6c
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.