Protocol detail

Structural Characterization of Tha-1 Homodimer

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To identify the HEPN domain within Tha, the HHpred web-server was used (https://toolkit.tuebingen.mpg.de/tools/hhpred, version 57c8707149031cc9f8edceba362c71a3762bdbf8). To analyse the structure of Tha-1, AlphaFold2^{26 (link)} and ColabFold v1.5.2^{27 (link)} were used to generate a model for the structure of the Tha-1-Tha-1 homodimer. The structure was analysed, and images were generated by PyMOL v2.5.4 (Schrödinger). The DALI web server (accessed 27 March 2023)^{28 (link)} searches against PDB90 (a collection of representative structures with less than 90% sequence identity from the PDB database) were performed for the truncated dimer (164–301).

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Rostøl J.T., Quiles-Puchalt N., Iturbe-Sanz P., Lasa Í, & Penadés J.R. (2024). Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles. Nature Microbiology, 9(5), 1312-1324.

Publication 2024

PyMOL v2.5.4

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Variable analysis

independent variables

Use of HHpred web-server to identify the HEPN domain within Tha
Use of AlphaFold2 and ColabFold to generate a model for the structure of the Tha-1-Tha-1 homodimer
Analysis of the structure of Tha-1-Tha-1 homodimer using PyMOL
Searches against PDB90 using the DALI web server for the truncated dimer (164–301)

dependent variables

Identification of the HEPN domain within Tha
Structure of the Tha-1-Tha-1 homodimer

control variables

Version of HHpred web-server used (version 57c8707149031cc9f8edceba362c71a3762bdbf8)
Version of ColabFold used (v1.5.2)
Version of PyMOL used (v2.5.4)
PDB90 database used for DALI web server searches

Annotations

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