Danbi Yoon, Ju Heun Moon, Anna Cho, Hyejoon Boo, Jeong Seok Cha*, Yoonji Lee*, and Jiho Yoo*. Mol. Cells 2023;46:337-44. https://doi.org/10.14348/molcells.2023.0001

Quercetin, a prevalent plant flavonoid, demonstrates many biological functions through its interaction with distinct protein targets. Recent structural investigations of protein–quercetin complexes have elucidated the molecular mechanism behind these actions. This paper presents a thorough structural analysis of experimentally established protein–quercetin complex structures published to date. The structure of the protein–quercetin complex elucidates the molecular mechanism by which quercetin influences protein function. These structures illustrate how quercetin’s chemical characteristics facilitate diverse modes of action by enabling particular interactions with the target protein. This structural knowledge provides the molecular foundation for comprehending quercetin’s biological roles and indicates avenues for future structural investigations of flavonoid–protein complexes, especially those with ambiguous molecular processes.

Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEα binary, and RNAP-TFEα-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEα bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEα interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEα interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEα and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs.

Inflammasomes are multi-protein complexes and play a crucial role in host defense against pathogens. Downstream inflammatory responses through inflammasomes are known to be related to the oligomerization degree of ASC specks, but the detailed mechanism still remains unexplored. Here, we demonstrate that oligomerization degrees of ASC specks regulate the caspase-1 activation in the extracellular space. A protein binder specific for a pyrin domain (PYD) of ASC (ASC^PYD) was developed, and structural analysis revealed that the protein binder effectively inhibits the interaction between PYDs, disassembling ASC specks into low oligomeric states. ASC specks with a low oligomerization degree were shown to enhance the activation of caspase-1 by recruiting and processing more premature caspase-1 through interactions between CARD of caspase-1 (caspase-1^CARD) and CARD of ASC (ASC^CARD). These findings can provide insight into controlling the inflammasome-mediated inflammatory process as well as the development of inflammasome-targeting drugs.

In Fig. 2, the HA–importin-α3 immunoprecipitation and corresponding Flag–NLS blots were inadvertently duplicated as the HA–importin-α5 immunoprecipitation and corresponding Flag–NLS blots. The two HA–importin-α5 blots have been replaced with the correct images in panel D in the figure shown below. There are no changes to the figure legend, which is accurate. This error does not affect the conclusions of the study.