21DI

Cryo-EM reconstruction of the cyanophage Pam5 small terminase

Summary for 21DI

• Entry DOI: 10.2210/pdb21di/pdb
• EMDB information: 67586
• Descriptor: Pam5 small terminase (1 entity in total)
• Functional Keywords: cyanophage, virus, viral protein, terminase
• Biological source: Pseudanabaena phage Pam5
• Total number of polymer chains: 9
• Total formula weight: 132553.57

Authors

Dong, D.Q.,Jiang, Y.L.,Zhou, C.Z. (deposition date: 2025-12-09, release date: 2026-04-22)

Primary citation

Dong, D.Q.,Yang, F.,Du, K.,Xu, K.,Cheng, W.B.,Chen, Y.,Zhou, C.Z.,Jiang, Y.L.
Structural and functional insights into the distinct DNA recognition mechanisms of the terminase small subunit TerS from cyanophages.
Acta Biochim.Biophys.Sin., 2026

PubMed Abstract: Efficient genome packaging is a critical step in the phage life cycle, directly influencing the viral maturation and infectivity. In tailed phages, this process is driven by a packaging motor composed of a portal protein and a terminase complex. The terminase complex usually consists of a large subunit (TerL) and a small subunit (TerS), which cooperate to recognize, cleave, and translocate genomic DNA into the capsid. However, due to the remarkable diversity and complexity of phage packaging systems, the molecular mechanisms governing TerS-mediated DNA recognition remain poorly understood. Here, we report the 3.51 Å cryo-electron microscopy structure of the TerS from the short-tailed cyanophage Pam5, which infects the host Chao 1806. Pam5 TerS assembles into a nonameric ring with a radially symmetric spiral architecture. Biochemical assays show that Pam5 TerS recognizes the genomic DNA via a specific interaction between the N-terminal helix-turn-helix (HTH) domain of TerS and a 21-bp DNA sequence within the gene. In contrast, the TerS from another short-tailed cyanophage, Pam1, which infects the same host, binds to DNA in a sequence-independent manner. These findings reveal that cyanophages, even infecting the same host, could adopt two distinct DNA recognition strategies: HTH-mediated sequence-dependent or sequence-independent modes. This work provides structural and mechanistic insights into the diverse DNA-recognition strategies of TerS and advances our understanding of the evolutionary plasticity of viral genome packaging mechanisms.

PubMed: 41865250
DOI: 10.3724/abbs.2026042

Experimental method

ELECTRON MICROSCOPY (3.5 Å)