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. 2008 Apr 30;3(4):e2119. doi: 10.1371/journal.pone.0002119

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Proell et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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A Apaf-1 structure and domain organization. Apaf-1ΔWD40 (PDB id: 1z6t) is shown in ribbon representation color-coded according to domain boundaries (CARD aa 1–101, NACHT-GxP aa108–365, WH aa366–450, and SH aa451–586. ADP molecule bound to the active site is shown in sphere representation. B Evolutionary tree of human NLR NACHT-WH domain generated for NLR proteins and orthologues. Labels correspond to the accession numbers (Uniprot) Mm_1: Q3TAU8, Mm_2: Q2LKU8, Mm_3: Q2LKU9, Mm_4: Q2LKV8, Mm_5: A1Z198; NALP5_m: NALP5_MOUSE, Mm_6: Q4PLSO, Mm_7: Q66JP4; Mm_8: NAL4C_MOUSE, Mm_9:Q08EE9, Mm_10: Q8R4B8. Dr_1: A5PEZ1; Dr_2: A3KQD4, Dr_3: Q1AMZ9, Xl_1: Q28DS5, Xl_2: Q6GNU6. Black lines indicate a probability of more than 50%, blue lines indicate a 95% confidence in the grouping, and red lines indicate a confidence below the 40%. Green fonts indicate human proteins, black fonts alternative organisms. Mm and _m is Mus musculus (mouse), Dr and _Dr is Danio rerio (fish), Xl and _Xl is Xenopus leavis (frog). Orange fonts indicate an “S” in the Walker A motif in human sequences. Circles and modified ovals over the clades indicate the type of domain present at the N-terminal region of the NACHT domain. PYD is Pyrin domain, CARD is Card domain, Card? indicates CARD-like and BIR are BIR repeats. Apaf-1 is used to root the tree.