RSS

PDB:2R9R

Protein Name

Paddle-chimaera K+ channel

Species

Rat

Biological Context

Some membrane proteins detect membrane potential, the potential difference between extracellular and intracellular regions, and change their structure accordingly. These are, for example, voltage-dependent ion channels, voltage-dependent proton channels, and voltage-regulated enzymes, among which major amino acids of the voltage sensor are conserved. The voltage sensor is a membrane protein domain with charged amino acids and its voltage-dependent conformational change leads to a gating of the pore region.

Structure Description

2r9r2r9r_x2r9r_y

A crystal structure of a paddle-chimaera K+ channel, Kv2.1 channel with a voltage-sensor paddle of Kv1.2, has been determined (Fig. 1, 2). This structure shows an open conformation and four potassium ions are observed at the center of the paddle-chimaera channel (Fig. 2). The voltage-sensor paddle is a helix-turn-helix structural motif composed of S3b and S4 helices. Voltage sensors are molecular volt meters that read the membrane voltage and regulate the pore. Generally, potassium ion channels form tetramers in which a pore region is centered with potassium ions and four voltage sensors surround the pore. The paddle-chimaera channel also showed good similarity with other K+ channels. Additionally, this crystal structure was constructed under a mixture of phospholipids and detergents to provide a membrane-like environment. Lipid molecules form bilayer-like arrangement, especially in the outer leaflet part (Fig. 3).

 There are many charged residues in the voltage sensors which are embedded in hydrophobic cell membranes (Fig. 4). Negatively charged amino acids in the voltage sensor are divided into two clusters: an external negative cluster consisting of glutamate 183 and 226, and an internal negative cluster consisting of glutamate 154, 236, and aspartate 259. On the other hand, positively charged amino acids are aligned on the S4 helix (R0, R1, R2, R3, R4, K5 and R6, from extracellular to intracellular regions). R3 and R4 form hydrogen bonds with the external negative cluster. Besides, phenylalanine 233 is one of most conserved residues and separates negative clusters (Fig. 4).

A hypothesis for the gating mechanism was proposed. Voltage sensor paddles switches their interaction partners between the two negative clusters depends on the membrane voltage. The large paddle movement across the membrane results in the charge of the pore structure. However it should be noted that how the paddles overcome an energy barrier at the phenylalanine 233 is still unknown. So, a closed structure is needed to reveal new interactions on the S4 helix.

paddle_chimaera_channel (Fig. 1) paddle-chimaera channel.
The red regions are the transferred voltage sensors from Kv2.1 channels. Remaining lightblue structures are α subunits of Kv1.2 channels. β subunits of Kv1.2 channels are colored with orange. Both subunits forms homotetramer structures and the whole channel complexes result in octamer. Voltage paddles are in the transmembrane region (see Fig. 3) and potassium ions (green spheres) are located in the central pore region of the channel. This structure shows an open conformation.

The extracellular region is on the top and intracellular bottom.
an_alpha_subunit (Fig. 2) α subunit of the paddle-chimaera channel.
Four potassium ions (green spheres) are located at the pore region.
The paddle-chimaera (red) is the S3b-S4 helix-turn-helix region.
lipids (Fig. 3) Lipids in the structure.
Lipid molecules are shown by CPK representation, colored according to atom type: yellow, carbon; red, oxygen; orange, phosphorous). The paddle-chimaera channel is in ribbon representation (lightblue).

The extracellular region is on the top and intracellular bottom.

Particularly, lipids at extracellular leaflet are in the membrane-like arrangement.
voltage_sensor (Fig. 4) Voltage sensor.
Blue line is an α subunit of paddle-chimaera channel. Green spheres are potassium ions.

The voltage-sensor paddle is composed from S3b and S4 helices.Positively charged residues on S4 are colored with yellow. These are numbered from the extracellular (top) part as R0, R1, R2, R3, R4, K5 and R6.
The voltage sensor region has two negatively charged clusters (red): extracellular one (E183, E226) and intracellular one (E154, E236, D259). On this open conformation, hydrogen bonds are made between extracellular negative cluster and R3, R4 positive residues. There is highly conserved phenylalanine 233 (green) between two clusters.

It is estimated that a movement of S4 to intracellular region makes new interactions between S4 positive residues and intracellular negative cluster when the channel close.

Protein Data Bank (PDB)

References

Source

Long, S.B. Tao, X. Campbell, E.B. MacKinnon, R.; "Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment."; Nature; (2007) 450:376-382 PubMed:18004376.

Others

author: Naoya Fujita


Japanese version:PDB:2R9R