Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions

Zhu, Dahuan; Wang, Xiangxi; Fang, Qianglin; Etten, James L. Van; Rossmann, Michael G.; Rao, Zihe; Zhang, Xinzheng

doi:10.1038/s41467-018-04051-9

Cited by 98 publications

(124 citation statements)

References 42 publications

(41 reference statements)

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“…1D, S1 and S2). By using the block-reconstruction method (Yuan et al, 2018;Zhu et al, 2018a), we were able to improve the resolution for the structures of the hexameric and dodecameric terminases to 3.5 Å and 3.6 Å, respectively, suggesting that the complex is intrinsically flexible with unrestrained symmetry (Figs. 1D, S2 and Table S1).…”

Section: Resultsmentioning

confidence: 99%

“…To further improve resolution we used the block-based reconstruction (Wang et al, 2018;Yuan et al, 2018;Zhu et al, 2018a;Wang et al, 2019). The orientation parameters of each particle image (hexamer and dodecamer) determined in Relion were used to guide extraction of the block region (∼50% bigger than monomer) and the block was refined and reconstructed (Scheres, 2012).…”

Section: Image Processingmentioning

confidence: 99%

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Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation

et al. 2020

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Genome packaging is a fundamental process in a viral life cycle and a prime target of antiviral drugs. Herpesviruses use an ATP-driven packaging motor/terminase complex to translocate and cleave concatemeric dsDNA into procapsids but its molecular architecture and mechanism are unknown. We report atomic structures of a herpesvirus hexameric terminase complex in both the apo and ADP•BeF3-bound states. Each subunit of the hexameric ring comprises three components-the ATPase/terminase pUL15 and two regulator/fixer proteins, pUL28 and pUL33-unlike bacteriophage terminases. Distal to the nuclease domains, six ATPase domains form a central channel with conserved basicpatches conducive to DNA binding and transacting arginine fingers are essential to ATP hydrolysis and sequential DNA translocation. Rearrangement of the nuclease domains mediated by regulatory domains converts DNA translocation mode to cleavage mode. Our structures favor a sequential revolution model for DNA translocation and suggest mechanisms for concerted domain rearrangements leading to DNA cleavage. KEYWORDS dsDNA virus, genome packaging, viral maturation, terminase complex, drug target Yunxiang Yang and Pan Yang contributed equally to this work.

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Section: Resultsmentioning

confidence: 99%

Section: Image Processingmentioning

confidence: 99%

Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation

et al. 2020

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“…Recently, a 3.5 Å near-atomic resolution structure of PBCV-1 by cryoEM was reported [64]. This resolution was accomplished by correcting for the Ewald sphere effect in single cryoEM reconstructions [65]. Otherwise, the technology was stalled at~4.5 Å resolution.…”

Section: Algal Virusesmentioning

confidence: 99%

Chloroviruses

Etten

Agarkova

Dunigan

2019

Viruses

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Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.

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“…To resolve the symmetry mismatch between the portal (C12) and the capsid (C5), the previously described sub-particle reconstruction and symmetry relaxation procedures 15,51,52 were employed as follows. The alignment and CTF parameters of each sub-particle around the portal vertex were recalculated based on the corresponding values of their original particles (or "parental particles"), previously determined when calculating the 5-fold-symmetric reconstruction of the capsid.…”

Section: Methodsmentioning

confidence: 99%

Structural morphing in a symmetry-mismatched viral vertex

et al. 2020

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Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of asymmetry, a 12-fold-symmetric dodecameric portal complex inserted into a 5-fold-symmetric capsid vertex, is found in numerous icosahedral viruses, including tailed bacteriophages, herpesviruses, and archaeal viruses. This vertex is critical for driving capsid assembly, DNA packaging, tail attachment, and genome ejection. Here, we report the near-atomic in situ structure of the symmetry-mismatched portal vertex from bacteriophage T4. Remarkably, the local structure of portal morphs to compensate for symmetry-mismatch, forming similar interactions in different capsid environments while maintaining strict symmetry in the rest of the structure. This creates a unique and unusually dynamic symmetry-mismatched vertex that is central to building an infectious virion.

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Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions

Cited by 98 publications

References 42 publications

Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation

Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation

Chloroviruses

Structural morphing in a symmetry-mismatched viral vertex

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