Protocol for the purification and crystallization of the Drosophila melanogaster Cfp1PHD domain in complex with an H3K4me3 peptide
Bibliographic record
Abstract
The tri-methylation of histone H3 on K4 (H3K4me3) is a key epigenetic modification that is predominantly found at active gene promoters and is deposited by the complex of proteins associated with SET1 (COMPASS). CXXC zinc finger protein 1 (Cfp1) regulates this process by recruiting SET1 to chromatin and recognizing H3K4me3 via its plant homeodomain (Cfp1 PHD ). Here, we present a protocol for the purification and crystallization of the Drosophila melanogaster Cfp1 PHD domain in complex with an H3K4me3 peptide (PDB: 9C0O). We describe steps for obtaining highly pure Cfp1 PHD and diffraction-quality crystals. We then detail procedures for rapidly identifying crystals containing the H3K4me3-bound form of the Cfp1 PHD domain. For complete details on the use and execution of this protocol, please refer to Grégoire et al. 1 • Production and purification of Cfp1 PHD using affinity chromatography • Crystallization and structure determination of Cfp1 PHD • Detailed troubleshooting to solve the H3K4me3-bound form of Cfp1 PHD • Structural characterization of Cfp1 PHD bound to H3K4me3 Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. The tri-methylation of histone H3 on K4 (H3K4me3) is a key epigenetic modification that is predominantly found at active gene promoters and is deposited by the complex of proteins associated with SET1 (COMPASS). CXXC zinc finger protein 1 (Cfp1) regulates this process by recruiting SET1 to chromatin and recognizing H3K4me3 via its plant homeodomain (Cfp1 PHD ). Here, we present a protocol for the purification and crystallization of the Drosophila melanogaster Cfp1 PHD domain in complex with an H3K4me3 peptide (PDB: 9C0O). We describe steps for obtaining highly pure Cfp1 PHD and diffraction-quality crystals. We then detail procedures for rapidly identifying crystals containing the H3K4me3-bound form of the Cfp1 PHD domain.
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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 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".