PLIC: Database of 3D Aligned P-Loop Ion Channels with universal residue Labels

Purpose

The superfamily of P-loop channels includes potassium, sodium, calcium, cyclic-nucleotide gated, two-pore, and transit receptor potential channels, as well as ionotropic glutamate receptors. Despite the large functional diversity, all members of the superfamily have conserved folding of transmembrane helices in the tetrameric or pseudo-tetrameric pore-forming module where each monomer has either two (2TM) or six (6-TM) transmembrane segments. 6-TM channels also have conserved folding of voltage-sensing domains. Hundreds of atomic-scale structures of P-loop channels obtained by X-ray crystallography and cryo-electron microscopy are deposited in the Protein Data Bank and the number of structures rapidly increases. Comparative structural analysis of P-loop channels is desirable, but it is hindered due different residue numbers, ambiguous sequence alignments, and different 3D orientation of the structures. To overcome these problems, we elaborated a universal residue-labeling scheme for P-loop channels and sequence alignments of transmembrane segments that is consistent with this scheme.

Residue labeling

A universal residue labeling in TM segments is a key feature of our database that may facilitate structural comparison of the vastly different P-loop channels (Figure). P-loop channels are tetramers or pseudo-tetramers. Four subunits in the tetrameric channels are labeled as chains A to D, like in many PDB structures. In pseudo-tetrameric channels, such as sodium and calcium channels, repeats I to IV of the pore-forming α subunit are also labeled as chains A, B, C, and D. Ancillary subunits of these channels (if any) are labeled as chains E, F, G, etc. in the order they appear in the original PDB file. Ions are labeled as chain I (ion), low-molecular weight ligands are labeled as chain L (ligands). Water molecules are labeled as chain W. Residues in the ancillary subunits are numbered as in the original PDB file. Ligands, ions, and waters are numbered sequentially, as they appear in the PDB file. In all tetrameric channels, chains A to D are arranged clockwise when viewed from the extracellular space to match the arrangement of repeats I to IV, respectively, in sodium channels.

A residue label in a TM segment of the pore domain consists of two parts. The first part contains a letter indicating chain A-D, which may be omitted and number 1 to 6 that indicate, respectively, segments S1 to S6. Number 7 refers to the long chain C-terminal to S6, which is seen in some channels, e.g., inter-repeat cytoplasmic linkers or C-terminal parts. Three digits in the second part of the label indicate a relative residue number. The numbers are counted from the most conserved residues in the TM segment, which is assigned number 550. The big numbers are chosen with the aim to accommodate extra- and intracellular loops, which are very large in some channels, or the N-terminal chain. P-loops are not TM segments. In 6-TM channels they are located between segments S5 and S6. In 2TM channels P-loops are located between segments S1 and S2. We assigned number 5.850 to the valine residue in the conserved motif TVGYG (the signature sequence) in the selectivity filter of potassium channels. Since loops are vastly different, no attempt was made to perform their sequence alignment. N-ends of the intracellular and extracellular loops S1-S2, S2-S3, S3-S4, S5-P1 and P2-S6 are assigned, respectively, numbers 1.600, 2.600, 3.600, 5.600 and 5.900 (Figure). Sequence alignment of TM segments was initially performed by Clustal Omega and was manually corrected. First, we avoided insertions and deletions in the alignment within helical segments. Corrections were also made to provide the same orientation of the helix residues in homologous positions. We are unaware of P-loop channels whose residue labels would not fit into this general scheme.

Processing 3D structures.

Original data are downloaded from the Protein Data Bank (www.rcsb.org). The PDB files deposited as “Biological assembly” were used. To obtain 3D-aligned structures we used as a template the X-ray structure 2R9R of the Kv1.2-Kv2.1 chimeric potassium channel in the open state. The structure was initially reoriented in such a way that the pore axis coincided with the z axis and whose coordinates increased in the extracellular direction. The xOy plane accommodated the backbone oxygens in position 5.850. Other structures were aligned to the reference structure 2R9R by minimizing RMS deviations between alpha carbons in positions 5.838 – 5.847 in the P1 helix, which is the most structurally conserved element in P-loop channels. This strategy of 3D alignment seems to have significant advantage over the alignment of full-length channels. In the latter case in may be difficult to locate in 3D aligned structures rather subtle, but functionally significant differences.

Usage

The relabeled and 3D-aligned structures are grouped in the folders according to the channels families. The structures can be viewed at the site or downloaded from it. Each entry also contains the references to original structure at the Protein Data Bank and to the original publication at PubMed. There are three ways to find the structures. 1. Direct catalog browsing (left panel of the navigation page). 2. Tags that extract the corresponding group of structures (right pane on the navigation page). 3. Search engine (top of the navigation page).

Tools

The database contains a utility that allows a user to renumber and 3D-align new structures of P-loop channels.

Download

You can download our alignment in an Excel format via this link!

Feedback

The authors welcome comments, corrections and suggestions. New structures can be included by request. You can learn more about us and how to contact us here.

Updates

Nothing new yet.