PDBsum entry 6ibc

Virus

PDB id: 6ibc

Contents

Protein chains

(+ 0 more) 374 a.a.

345 a.a.

PDB id:

6ibc

Name:

Virus

Title:

Thermophage p23-45 procapsid

Structure:

Major head protein. Chain: a, b, c, d, e, f, g

Source:

Thermus virus p23-45. Organism_taxid: 466051. Cell_line: thermus thermophilus hb8

Authors:

O.W.Bayfield,E.Klimuk,D.C.Winkler,E.L.Hesketh,M.Chechik,N.Cheng, E.C.Dykeman,L.Minakhin,N.A.Ranson,K.Severinov,A.C.Steven,A.A.Antson

Key ref:

O.W.Bayfield et al. (2019). 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. PubMed id: 30737287 DOI: 10.1073/pnas.1813204116

Date:

29-Nov-18 Release date: 13-Feb-19

Protein chains

A7XXC2  (A7XXC2_9CAUD) -  Major capsid protein from Thermus virus P23-45

Seq: 409 a.a.

Struc: 374 a.a.

Protein chain

A7XXC2  (A7XXC2_9CAUD) -  Major capsid protein from Thermus virus P23-45

Seq: 409 a.a.

Struc: 345 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G: E.C.?

DOI no: 10.1073/pnas.1813204116

Proc Natl Acad Sci U S A 116:3556-3561 (2019)

PubMed id: 30737287

Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids.

O.W.Bayfield, E.Klimuk, D.C.Winkler, E.L.Hesketh, M.Chechik, N.Cheng, E.C.Dykeman, L.Minakhin, N.A.Ranson, K.Severinov, A.C.Steven, A.A.Antson.

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 Thermus thermophilus 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.