PDBsum entry 3kvt

Potassium channel

PDB id: 3kvt

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-gated potassium channel

Structure:

Potassium channel protein shaw. Chain: a. Fragment: tetramerization (t1) domain. Engineered: yes. Mutation: yes. Other_details: one zn2+ per monomer tetrahedrally coordinated at 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.Pfaffinger, 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

Protein chain

O76457  (O76457_APLCA) -  Shaw potassium channel Kv3.1a from Aplysia californica

Seq: 514 a.a.

Struc: 103 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

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.