Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 116, Issue 9, Page 3556-3561, Year 2019
Publish date	Feb 26, 2019
Authors	Oliver W Bayfield / Evgeny Klimuk / Dennis C Winkler / Emma L Hesketh / Maria Chechik / Naiqian Cheng / Eric C Dykeman / Leonid Minakhin / Neil A Ranson / Konstantin Severinov / Alasdair C Steven / Alfred A Antson /
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 ...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.
External links	Proc Natl Acad Sci U S A / PubMed:30737287 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.95 - 9.56 Å
Structure data	4433 6i9e EMDB-4433: Thermophage P23-45 empty expanded capsid icosahedral reconstruction PDB-6i9e: Thermophage P23-45 empty expanded capsid Method: EM (single particle) / Resolution: 3.74 Å EMDB-4445: Thermophage P23-45 procapsid asymmetric reconstruction Method: EM (single particle) / Resolution: 9.33 Å EMDB-4446: Thermophage P23-45 empty expanded capsid C5 reconstruction Method: EM (single particle) / Resolution: 9.56 Å 4447 6ibc EMDB-4447: Thermophage P23-45 procapsid icosahedral reconstruction PDB-6ibc: Thermophage P23-45 procapsid Method: EM (single particle) / Resolution: 4.39 Å PDB-6ibg: Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus Method: X-RAY DIFFRACTION / Resolution: 1.95 Å
Chemicals	ChemComp-MPD: (4S)-2-METHYL-2,4-PENTANEDIOL / precipitantYM / 2-Methyl-2,4-pentanediol ChemComp-HOH*: WATER / Water
Source	thermus virus p23-45 Thermus phage P2345 (virus)
Keywords	VIRUS / bacteriophage / thermophage / caudovirales / siphoviridae / capsid / auxiliary / HK97 / procapsid / VIRAL PROTEIN