EMAN2: an extensible image processing suite for electron microscopy.

Adenovirus serotype 5 hexon mediates liver gene transfer

1We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a Variable-metric gradient Descent algorithm with Adaptive Moments estimation, for image refinement; a convolutional neural network for unsupervised selection of 2D classes; and a flexible framework for the design and execution of multiple jobs in pre-defined workflows. In addition, we present a stand-alone utility called MDCatch that links the execution of jobs within this framework with metadata gathering during microscope data acquisition. The new tools are aimed at providing fast and robust procedures for unsupervised cryo-EM structure determination, with potential applications for on-the-fly processing and the development of flexible, high-throughput structure determination pipelines. We illustrate their potential on twelve publicly available cryo-EM data sets.

/pdf/new-tools-for-automated-cryo-em-single-particle-analysis-in-4lnlxvn1zw.pdf

New tools for automated cryo-EM single-particle analysis in RELION-4.0

The three-dimensional structure of the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid. This study reports the use of electron microscopy to reconstruct a large, 3-megadalton complex of the bacterial type IV secretion (T4S) system from Escherichia coli, made up of eight proteins assembled in an intricate stoichiometric relationship to form a stalk spanning the membrane to unite a core outer-membrane-associated complex with an inner membrane complex. The structure reveals a novel architecture that differs markedly from those known from other bacterial secretion systems. T4S systems are used by many bacterial pathogens to deliver virulence factors and to transfer genetic material and also show potential as a tool for the genetic modification of human cells. Bacterial type IV secretion systems translocate virulence factors into eukaryotic cells1,2, distribute genetic material between bacteria and have shown potential as a tool for the genetic modification of human cells3. Given the complex choreography of the substrate through the secretion apparatus4, the molecular mechanism of the type IV secretion system has proved difficult to dissect in the absence of structural data for the entire machinery. Here we use electron microscopy to reconstruct the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid. We show that eight proteins assemble in an intricate stoichiometric relationship to form an approximately 3 megadalton nanomachine that spans the entire cell envelope. The structure comprises an outer membrane-associated core complex1 connected by a central stalk to a substantial inner membrane complex that is dominated by a battery of 12 VirB4 ATPase subunits organized as side-by-side hexameric barrels. Our results show a secretion system with markedly different architecture, and consequently mechanism, to other known bacterial secretion systems1,4,5,6.

/pdf/structure-of-a-type-iv-secretion-system-55qzc7fyed.pdf

Structure of a type IV secretion system

Two-dimensional (2D) crystalline materials possess unique structural, mechanical and electronic properties that make them highly attractive in many applications. Although there have been advances in preparing 2D materials that consist of one or a few atomic or molecular layers, bottom-up assembly of 2D crystalline materials remains a challenge and an active area of development. More challenging is the design of dynamic 2D lattices that can undergo large-scale motions without loss of crystallinity. Dynamic behaviour in porous three-dimensional (3D) crystalline solids has been exploited for stimuli-responsive functions and adaptive behaviour. As in such 3D materials, integrating flexibility and adaptiveness into crystalline 2D lattices would greatly broaden the functional scope of 2D materials. Here we report the self-assembly of unsupported, 2D protein lattices with precise spatial arrangements and patterns using a readily accessible design strategy. Three single- or double-point mutants of the C4-symmetric protein RhuA were designed to assemble via different modes of intermolecular interactions (single-disulfide, double-disulfide and metal-coordination) into crystalline 2D arrays. Owing to the flexibility of the single-disulfide interactions, the lattices of one of the variants ((C98)RhuA) are essentially defect-free and undergo substantial, but fully correlated, changes in molecular arrangement, yielding coherently dynamic 2D molecular lattices. (C98)RhuA lattices display a Poisson's ratio of -1-the lowest thermodynamically possible value for an isotropic material-making them auxetic.

/pdf/self-assembly-of-coherently-dynamic-auxetic-two-dimensional-3r47i1528o.pdf

Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals

Bsoft: Image and Molecular Processing in Electron Microscopy

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Bsoft: Image and Molecular Processing in Electron Microscopy