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TitleAlphaFold 3-powered discovery of phage proteins that inhibit bacterial transcription initiation.
Journal, issue, pagesCell Rep, Vol. 45, Issue 3, Page 117082, Year 2026
Publish dateMar 24, 2026
AuthorsLinggang Yuan / Qingyang Liu / Xiaojian Xiao / Liqiao Xu / Liang Liang / Yang Guo / Yue Yao / Hui Wang / Youjun Feng / Xiaoting Hua / Yu Feng /
PubMed AbstractMany phages encode proteins that specifically inhibit host RNA polymerase activity, thereby sabotaging and, in some cases, hijacking the host transcription machinery to serve their needs. Traditional ...Many phages encode proteins that specifically inhibit host RNA polymerase activity, thereby sabotaging and, in some cases, hijacking the host transcription machinery to serve their needs. Traditional methods for identifying new phage proteins that inhibit bacterial transcription are labor intensive and require access to live phages. To overcome these limitations, we develop a highly efficient pipeline for AlphaFold 3-guided discovery of phage proteins that inhibit bacterial transcription initiation. Using this pipeline, three phage proteins are identified and characterized. Structural and biochemical analyses demonstrate that these phage proteins bind to distinct sites on RNA polymerase and inhibit transcription initiation via different mechanisms. This study showcases the power of AlphaFold 3 in discovering novel binders of large protein complexes, and the pipeline developed here could be readily adapted to screen modulators of other large targets, such as the ribosome, proteasome, and CRISPR-Cas systems.
External linksCell Rep / PubMed:41824451
MethodsEM (single particle)
Resolution3.3 - 4.0 Å
Structure data

65597

9w3d

EMDB-65597, PDB-9w3d:
Cryo-EM structure of E. coli RNA polymerase in complex with EP1
Method: EM (single particle) / Resolution: 4.0 Å

65598

9w3e

EMDB-65598, PDB-9w3e:
Cryo-EM structure of E. coli RNA polymerase in complex with PP1
Method: EM (single particle) / Resolution: 3.6 Å

65600

9w3g

EMDB-65600, PDB-9w3g:
Cryo-EM structure of E. coli RNA polymerase in complex with VP1
Method: EM (single particle) / Resolution: 3.3 Å

Source
  • escherichia coli (E. coli)
  • escherichia phage phisusp1 (virus)
  • pseudomonas phage vb_paem_pao1_ab17 (virus)
  • escherichia coli (strain k12) (bacteria)
  • vibrio phage vb_vpap_m3 (virus)
KeywordsTRANSCRIPTION / AlphaFold 3 / transcription regulation / phage / RNA polymerase / sigma factor

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