6IBG

Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus

Summary for 6IBG

• Entry DOI: 10.2210/pdb6ibg/pdb
• Descriptor: Portal protein, (4S)-2-METHYL-2,4-PENTANEDIOL (3 entities in total)
• Functional Keywords: bacteriophage, thermophage, caudovirales, siphoviridae, capsid, auxiliary, hk97, virus, viral protein
• Biological source: Thermus virus P23-45
• Total number of polymer chains: 3
• Total formula weight: 148520.47

Authors

Bayfield, O.W.,Klimuk, E.,Winkler, D.C.,Hesketh, E.L.,Chechik, M.,Cheng, N.,Dykeman, E.C.,Minakhin, L.,Ranson, N.A.,Severinov, K.,Steven, A.C.,Antson, A.A. (deposition date: 2018-11-30, release date: 2019-01-23, Last modification date: 2024-06-19)

Primary citation

Bayfield, O.W.,Klimuk, E.,Winkler, D.C.,Hesketh, E.L.,Chechik, M.,Cheng, N.,Dykeman, E.C.,Minakhin, L.,Ranson, N.A.,Severinov, K.,Steven, A.C.,Antson, A.A.
Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids.
Proc. Natl. Acad. Sci. U.S.A., 116:3556-3561, 2019

PubMed Abstract: Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermostable bacteriophage, P23-45 of Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-Å and 4.4-Å resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-Å resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.

PubMed: 30737287
DOI: 10.1073/pnas.1813204116

Experimental method

X-RAY DIFFRACTION (1.95 Å)