The Arthropoda-specific Tramtrack group BTB protein domains use previously unknown interface to form hexamers
- Russian Academy of Sciences, Russian Federation
- King Abdullah University of Science and Technology, Saudi Arabia
Abstract
BTB (Bric-a-brack, Tramtrack and Broad Complex) is a diverse group of protein-protein interaction domains found within metazoan proteins. Transcription factors contain a dimerizing BTB subtype with a characteristic N-terminal extension. The Tramtrack group (TTK) is a distinct type of BTB domain, which can multimerize. Single-particle cryo-EM microscopy revealed that the TTK-type BTB domains assemble into a hexameric structure consisting of three canonical BTB dimers connected through a previously uncharacterized interface. We demonstrated that the TTK-type BTB domains are found only in Arthropods and have undergone lineage-specific expansion in modern insects. The Drosophila genome encodes 24 transcription factors with TTK-type BTB domains, whereas only four have non‑TTK‑type BTB domains. Yeast two-hybrid analysis revealed that the TTK-type BTB domains have an unusually broad potential for heteromeric associations presumably through dimer-dimer interaction interface. Thus, the TTK-type BTB domains are a structurally and functionally distinct group of protein domains specific to Arthropodan transcription factors.
Data availability
The cryo-EM maps (blushed-regularized and normal regularization) and PDB model files have been deposited in the Protein Data Bank under the PDB entry code 8RC6 and in the EMDB with entry code EMD-19049. SAXS data have been deposited in the Small Angle Scattering Biological Data Bank (www.sasbdb.org) under accession codes SASDP59 (merged data for LOLA1-120 at 1.0 mg/ml and 3.0 mg/ml), SASDP49 (CG67651-133 at 1.5 mg/ml). Atomic models (both native and exactly corresponding to expression constructs) and reports of SAXS approximation are provided as Supplemental files. Results of bioinformatic analysis are provided as Supplemental tables.
Article and author information
Author details
Konstantin I Balagurov
Konstantin M Boyko
Nikolai N Sluchanko
Funding
Russian Science Foundation (19-74-10099-P)
- Artem N Bonchuk
- Konstantin I Balagurov
- Konstantin M Boyko
- Anna D Burtseva
Russian Science Foundation (19-74-30026-Р)
- Artem N Bonchuk
- Konstantin I Balagurov
- Anastasia M Khrustaleva
- Olga V Arkova
- Karina K Khalisova
- Pavel G Georgiev
Ministry of Science and Higher Education of the Russian Federation (075-15-2019-1661)
- Artem N Bonchuk
- Konstantin I Balagurov
- Olga V Arkova
KAUST Baseline Grant (BAS/1/1107-01-01)
- Rozbeh Baradaran
- Andreas Naschberger
This work was supported by the Russian Science Foundation - project 19-74-10099-P to A.B. (expression and purification of proteins and their mutants), project 19-74-30026-Р to P.G. (analysis of protein-protein interactions) and by Ministry of Science and Higher Education of the Russian Federation - grant 075-15-2019-1661 (structural and bioinformatic analysis). Funding for open access charge: Ministry of Science and Higher Education of the Russian Federation and Russian Science Foundation. The single-particle cryo-EM work was financially supported by the KAUST Baseline Grant BAS/1/1107-01-01. N.N.S. and K.M.B. acknowledges that SEC-MALS work was supported by the Ministry of Science and Higher Education of the Russian Federation.
Copyright
© 2024, Bonchuk et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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The Arthropoda-specific Tramtrack group BTB protein domains use previously unknown interface to form hexamers
eLife 13:e96832.
https://doi.org/10.7554/eLife.96832
Further reading
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- Structural Biology and Molecular Biophysics
In eukaryotes, RNAs transcribed by RNA Pol II are modified at the 5′ end with a 7-methylguanosine (m7G) cap, which is recognized by the nuclear cap binding complex (CBC). The CBC plays multiple important roles in mRNA metabolism, including transcription, splicing, polyadenylation, and export. It promotes mRNA export through direct interaction with a key mRNA export factor, ALYREF, which in turn links the TRanscription and EXport (TREX) complex to the 5′ end of mRNA. However, the molecular mechanism for CBC-mediated recruitment of the mRNA export machinery is not well understood. Here, we present the first structure of the CBC in complex with an mRNA export factor, ALYREF. The cryo-EM structure of CBC-ALYREF reveals that the RRM domain of ALYREF makes direct contact with both the NCBP1 and NCBP2 subunits of the CBC. Comparing CBC-ALYREF with other cellular complexes containing CBC and/or ALYREF components provides insights into the coordinated events during mRNA transcription, splicing, and export.
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Under physiological conditions, proteins continuously undergo structural fluctuations on different timescales. Some conformations are only sparsely populated, but still play a key role in protein function. Thus, meaningful structure–function frameworks must include structural ensembles rather than only the most populated protein conformations. To detail protein plasticity, modern structural biology combines complementary experimental and computational approaches. In this review, we survey available computational approaches that integrate sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling techniques to derive all-atom structural models of rare protein conformations. We also propose strategies to increase the reliability and improve efficiency using deep learning approaches, thus advancing the field of integrative structural biology.
