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	Structural atlas of a human gut crassvirus.
Journal, issue, pages	Nature, Vol. 617, Issue 7960, Page 409-416, Year 2023
Publish date	May 3, 2023
Authors	Oliver W Bayfield / Andrey N Shkoporov / Natalya Yutin / Ekaterina V Khokhlova / Jake L R Smith / Dorothy E D P Hawkins / Eugene V Koonin / Colin Hill / Alfred A Antson /
PubMed Abstract	CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant ...CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss001, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.
External links	Nature / PubMed:37138077 / PubMed Central
Methods	EM (single particle)
Resolution	3.01 - 4.4 Å
Structure data	14088 7qof EMDB-14088, PDB-7qof: Icosahedral capsid of the phicrAss001 virion Method: EM (single particle) / Resolution: 3.01 Å 14089 7qog EMDB-14089, PDB-7qog: Portal protein assembly of the phicrAss001 virion with C12 symmetry imposed Method: EM (single particle) / Resolution: 3.09 Å 14090 7qoh EMDB-14090, PDB-7qoh: Unique vertex of the phicrAss001 virion with C5 symmetry imposed Method: EM (single particle) / Resolution: 3.32 Å 14091 7qoi EMDB-14091, PDB-7qoi: Unique vertex of the phicrAss001 virion Method: EM (single particle) / Resolution: 3.62 Å 14092 7qoj EMDB-14092, PDB-7qoj: Tail barrel assembly of the phicrAss001 virion with C12 symmetry imposed Method: EM (single particle) / Resolution: 3.21 Å 14093 7qok EMDB-14093, PDB-7qok: Tail muzzle assembly of the phicrAss001 virion with C6 symmetry imposed Method: EM (single particle) / Resolution: 3.38 Å 14094 7qol EMDB-14094, PDB-7qol: Tail assembly of the phicrAss001 virion with C6 symmetry imposed Method: EM (single particle) / Resolution: 3.33 Å EMDB-14100: Asymmetric reconstruction of the phicrAss001 virion Method: EM (single particle) / Resolution: 4.4 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-HOH: WATER / Water
Source	bacteroides phage crass001 (virus)
Keywords	VIRUS / crAssphage / bacteriophage / DNA virus / portal / connector / vertex / capsid / tail / muzzle / ring