Structure of the essential enzyme ThiM from the bacterium<i>Staphylococcus aureus</i>
Bibliographic record
Abstract
The human Early B-cell fctor (EBF) family of transcription factors plays a variety of developmental roles [1]. Roles for this four-member family of proteins (EBF1-4) include B-cell development in lymphopoiesis, neuronal development, osteogenesis, and adipogenesis. Furthermore, recent studies have started identifying the absence of expressed EBFs in different cancer forms such as leukemias (EBF1) and glioblastomas (EBF3), suggesting a new tumor suppressor role for EBF family members The structured part of the EBFs is composed of a DNA binding domain (DBD), a TIG (transcription factor immunoglobulin) domain, and an atypical helix-loop-helix (HLH) region. An additional unstructured trans-activation domain is also present in the C-terminus. The EBF proteins show very high homology within the family over the whole structured part, consequently they can bind to specific DNA response elements as homo or hetero-dimers. Although the different domains have been, to a certain extent, biochemically characterized, no structural information was yet available for the EBF proteins. Structural data is of particular importance for this family since they share very low sequence similarity with other transcription factors. Using a domain approach, we have independently solved both the DBD and TIG+HLH domains of human EBF1 and EBF3, respectively. Despite low sequence similarity, the DBD structure reveals a striking resemblance to the DNA binding domains of the Rel homology superfamily of transcription factors. Interesting features of this domain include an atypical zinc binding site, termed Zn-knuckle, a region previously coined as important for specific DNA binding and transcriptional activation The TIG+HLH domain reveals an interesting dimerisation motif likely involved in protein-protein interactions, with either family members or regulatory partners.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".