Table 1. Effective pore radii (r E) for several K+ channel crystals.
| Protein | PDB code | Crystal conditions & resolution |
Sphere radius (Å) |
Ref. | |||||
|---|---|---|---|---|---|---|---|---|---|
|
hollow |
Surf |
msms |
|||||||
| rE | rK | rE | rK | rE | rK | ||||
| Kv1.2/2.1 Paddle chimera | 2R9R | Complex with lipids at 2.4 Å | 5.2 | 4.4 | 4.5 | 3.7 | 4.4 | 3.6 | 7 |
| 4JTA | Complex with ChTx at 2.5 Å | 5.2 | 4.4 | 4.5 | 3.7 | 4.6 | 3.8 | 2 | |
| KvAP | 2A0L | 3.9 Å | 4.4 | 3.6 | 4.1 | 3.3 | 4.2 | 3.4 | 36 |
| 1ORQ | 3.2 Å | 4.9 | 4.1 | 5.1 | 4.3 | 5.5 | 4.7 | 37 | |
| MthK | 4HYO | 1.65 Å | 5.9 | 3.7 | 5.6 | 3.4 | 5.5 | 3.3 | 10 |
| 3LDC | 1.45 Å | 5.7 | 3.5 | 5.3 | 3.1 | 5.3 | 3.1 | 38 | |
| 1LNQ | 3.3 Å*** | 5.8 | 3.6 | 5.6 | 3.4 | 5.5 | 3.3 | 3 | |
| KcsA | 1K4C | 2.0 Å | 2.1 | <1.4 | <1.4 | 4 | |||
| 1BL8 | 3.2 Å | <1.4 | <1.4 | <1.4 | 5 | ||||
Surface calculation algorithms were used to define the cast envelope left by a spherical probe of varying radius22,23,24. A probe able to enter the pore from the channel’s cytosolic side created a continuous surface connecting the cytosolic face with the pore walls. However, when the probe cannot longer enter, it casts a bump in the place of the pore. Using this criterion, rE was defined as the largest sphere able to enter the pore. rK was calculated from Eq. (3). For Kv1.2/2.1 and KvAP we used rC = 0.8 Å16, while rC = 2.2 Å was used for MthK channels15. ChTx stand for charybdotoxin. ***The biological assembly of this structure is not fully symmetric at the pore entrance.