PDBsum entry 1s6c

Transport protein

PDB id: 1s6c

Contents

Protein chains

167 a.a. *

21 a.a. *

Metals

_CA ×2

Waters ×150

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural insights into the functional interaction of kchip1 with shal-Type k(+) channels.

Authors

W.Zhou, Y.Qian, K.Kunjilwar, P.J.Pfaffinger, S.Choe.

Ref.

Neuron, 2004, 41, 573-586. [DOI no: 10.1016/S0896-6273(04)00045-5]

PubMed id

14980206

Abstract

Four Kv channel-interacting proteins (KChIP1 through KChIP4) interact directly with the N-terminal domain of three Shal-type voltage-gated potassium channels (Kv4.1, Kv4.2, and Kv4.3) to modulate cell surface expression and function of Kv4 channels. Here we report a 2.0 Angstrom crystal structure of the core domain of KChIP1 (KChIP1*) in complex with the N-terminal fragment of Kv4.2 (Kv4.2N30). The complex reveals a clam-shaped dimeric assembly. Four EF-hands from each KChIP1 form each shell of the clam. The N-terminal end of Kv4.2 forming an alpha helix (alpha1) and the C-terminal alpha helix (H10) of KChIP1 are enclosed nearly coaxially by these shells. As a result, the H10 of KChIP1 and alpha1 of Kv4.2 mediate interactions between these two molecules, structurally reminiscent of the interactions between calmodulin and its target peptides. Site-specific mutagenesis combined with functional characterization shows that those interactions mediated by alpha1 and H10 are essential to the modulation of Kv4.2 by KChIPs.

Figure 3.
Figure 3. Structure of KChIP1*-Kv4.2N30(A) Stereo cylinder view of KChIP1* monomer showing the coordination of four EF-hands (helix 2 to 5, N lobe, in cyan; helix 6 to 9, C lobe, in blue) and the central groove bound by H10 (yellow) and α1 (red) helices. α1 is bent at Pro10. The N-terminal helix (H1) is shown in yellow.(B) Stereo view of the KChIP1*-Kv4.2N30 dimeric complex, which is 90° rotated around the horizontal axis from view A. The 2-fold axis lies at the center of the dimer and perpendicular to the paper. The molecules are colored in the same way as (A). The residues 21–30 of Kv4.2N30 lacking electron density are not shown. Dots represent residues 160–170 of KChIP1* that lack electron density. Calcium ions (spheres) are bound to EF-3 and EF-4.(C) Comparison of the loops from four EF-hands of KChIP1*. Canonical Ca^2+-coordinating positions are numbered (Figure 1A). Five out of seven Ca^2+-coordinating oxygens (red) are from side chains of four conserved residues (position 1, 3, 5, 12) and one from a backbone carboxy-group (position 7). Calcium-loaded EF-3 and EF-4 have an extra oxygen from water molecule. Position 1 of EF-1 is not shown because it is part of helix (E1). Blue atoms are nitrogens.

Figure 4.
Figure 4. Interactions between KChIP1* and α1 and the Common Binding Pocket Shared by NCS Proteins(A) Stereo view through the hydrophobic pocket of dimeric KChIP1*-Kv4.2N30 complex. The H1 and N lobe are colored in cyan and C lobe in black. H10 and α1 are green and brown ribbons, respectively. Trp8 (W8), Leu9 (L9), and Phe11 (F11) are three key residues interacting with hydrophobic pockets created by both subunits. Red residues from bottom subunit (N lobe) interact with W8 and F11 of α1 of the same subunit. Magenta residues from the top subunit (H10 and C lobe) interact with L9 of α1 of the bottom subunit. Phe81 (F81) and Phe82 (F82) in yellow from each subunit interact together to form the other hydrophobic cluster and sit next to H10-α1 helices. Red, magenta, and yellow residues form a hydrophobic pocket surrounding two central helices, H10 and α1. Bottom panel is the view rotated 85° around vertical axis from view A, showing how the N lobe of the bottom subunit and the C lobe of the top subunit together form the hydrophobic pocket. At the H10-α1 crossing point, side chains of Ala2 (A2), Ala3 (A3), and Ala6 (A6) of both α1 helices are displayed to show the close contacts.(B) Common binding pocket shared by NCS proteins. Surface maps, calculated from crystal structures with H10 (gray helices) excluded for comparison, display the central hydrophobic groove and conserved target binding pocket. All structures are Ca^2+ bound. KChIP1*-Kv4.2N30 is the only peptide bound binary complex structure, and the other three are just the Ca^2+ binding proteins by themselves. Polar surface residues are in gray and nonpolar surface residues are in yellow (inset). The binding pocket for Trp8 and Phe11 (W8/F11 Pocket) and the corresponding ones based on sequence homology on other NCS proteins are in red (same residues in red boxes in Figure 1 and Figure 4). The green helix is Kv4.2 α1 with W8 and F11 shown.

The above figures are reprinted by permission from Cell Press: Neuron (2004, 41, 573-586) copyright 2004.