Sandbox Reserved 1106

This Sandbox is Reserved from 25/11/2019, through 30/9/2020 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1091 through Sandbox Reserved 1115.

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Argonaut 1 (PDB 4KXT)

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D This is a default text for your page '. Click above on edit this page' to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia or to the article describing Jmol to the rescue. Structure Length and domains Primary Structure The Ago1 protein has the same 4 primary domains as all argonaut (N, PAZ, Mid, PIWI, describe in the page Argonaut) and the two linker regions L1 (also called DUF1785 domain) and L2. Indeed, there is 84% of similitudes between the primary sequence of hAgo1 and hAgo2. Besides the N domain is interacting with L1, L2 and PIWI domains via residues 18-48 and 138-173. Besides, Argonaut 1 can be found in a lot of phylogenetic groups, with different structure. For example, in the plant Brachypodium distachyon, where 10 argonauts proteins have been discovered, BdAGO1 lacks the N and Mid domains. This particularity explains the small size of this protein with only 624 residues. Moreover, BdAGO1 is related to Ago1 since the catalytic tetrad in the PIWI domain doesn’t work for it, enabling an endonuclease activity due to a missing of the last D/H residue However, the AtAGO1 (from Arabidopsis thaliana), which can be find in the nucleus and the cytoplasm of the plant, owns a Mid domain and its conformation is homologous to BdAO9, BdAGO11, BdAGO12, BdAGO15, and BdAGO16. On the other hand, BdAGO1 has AtAGO4 as its closest homolog (like BaAGO2, BdAGO3 and BdAGO4), even if the AtAGO4 possess a Mid Domain. Associated Proteins with Ago1 The Argonaute 1 protein can be associated with others molecular components of the cell. Therefore, proteomic analysis has demonstrated that RNase III Dicer binds hAgo1 through the PIWI domain (see page on argonaute) and also, at least, four other proteins in specific association with hAgo1: • TNRC6B isoform 1 / KIAA1093 (175kDa) which has RRM motif at C-term to recognize RNA, and also GW repeats (trinucleotide motifs) • MOV10 (130kDa) • PRMT5 (arginine methyl-transferase) (70kDa) • And, with more doubts, the translation factor eEF1α (50kDa) hAgo1 in a complex with let-7 The hAgo1 interact with an endogenous let-7 in a homologous manner as hAgo2 interact with miR20a, but with some slightly differences. From a domain point of view, the position of L1 linker is the same for hAgo1/let-7 and hAgo2/miR20a, as well as the N subdomain (from residues K49 to S137 of the N domain) interaction with the endogenous sequence is the globally the same for both Ago1 and hAgo2 except a 3A translation toward the PIWI domain in hAgo1. Besides the piece of information gets from the N subdomain may suggest an interaction with the guide-target duplexes. On the other hand, the PAZ domain is folded differently in hAgo1/let-7 in order to be placed away from the PIWI domain. Then, from a nucleotide point of view, hAgo1 shows 6 RNA-specific interactions with ribose 2’OH of let-7 (U1, G2, G4, G5, A7 and A8). There are either direct or water-mediated through the side- or main- chain atoms of hAgo1 like for hAgo2/miR20a. However, there is one interaction presents in hAgo2/miR20a that is missing in hAgo1/let-7 ; it is the one with U6 since this base is slightly modified because of the shift of α7 in the L2 toward the N domain. Furthermore, the first adenine base has a syn conformation around the glycosidic bond and the last two bases are piled in the PAZ domain (à verifier) Finally, one of the most important aspect is the non-5’ phosphorylated strand ; indeed the U1 base of let-7 and the 5’P of hAgo1 are interacted with protein residues of the Mid and PIWI domains which avoid an interaction between them, preventing a phosphorylation which is important for accurate slicing activity (see: part 2.a). Knowing that the nine first 9 nucleotids of let-7 are: 5’AAUAUUAAA3’. Structural highlights This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.