PDBsum entry 1r3k

Membrane protein

PDB id: 1r3k

Contents

Protein chains

212 a.a. *

219 a.a. *

103 a.a. *

Ligands

DGA

Metals

_TL ×3

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The occupancy of ions in the k+ selectivity filter: charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates.

Authors

Y.Zhou, R.Mackinnon.

Ref.

J Mol Biol, 2003, 333, 965-975. [DOI no: 10.1016/j.jmb.2003.09.022]

PubMed id

14583193

Abstract

Potassium ions diffuse across the cell membrane in a single file through the narrow selectivity filter of potassium channels. The crystal structure of the KcsA K+ channel revealed the chemical structure of the selectivity filter, which contains four binding sites for K+. In this study, we used Tl+ in place of K+ to address the question of how many ions bind within the filter at a given time, i.e. what is the absolute ion occupancy? By refining the Tl+ structure against data to 1.9A resolution with an anomalous signal, we determined the absolute occupancy of Tl+. Then, by comparing the electron density of Tl+ with that of K+, Rb+ and Cs+, we estimated the absolute occupancy of these three ions. We further analyzed how the ion occupancy affects the conformation of the selectivity filter by analyzing the structure of KcsA at different concentrations of Tl+. Our results indicate that the average occupancy for each site in the selectivity filter is about 0.63 for Tl+ and 0.53 for K+. For K+, Rb+ and Cs+, the total number of ions contained within four sites in the selectivity filter is about two. At low concentrations of permeant ion, the number of ions drops to one in association with a conformational change in the selectivity filter. We conclude that electrostatic balance and coupling of ion binding to a protein conformational change underlie high conduction rates in the setting of high selectivity.

Figure 5.
Figure 5. The selectivity filter conformation in A 3 mM K⁺ or B 25 mM Tl⁺. Both structures are presented the same way as in Figure 1B and C.

Figure 7.
Figure 7. Transition between low- and high-ion structures may be important for high conduction rates. A, Experimentally observed conformational change when the occupancy in the selectivity filter changes from 1.0 to 2.0 ions. B, In a hypothetical case, the selectivity filter is held in a pre-formed, high-ion structure. Two ions will bind with lower affinity if binding energy is used to perform work to change the protein's conformation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 333, 965-975) copyright 2003.