Structure of a canonical RNase YoeB bound to the ribosome

As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3'-phosphate at the newly formed 3' end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity.

Different teaching way to space group and symmetry operation: polyhedral vs ball

To introduce the regulations of space group combining with a symmetry operation, put an orientation ball at a position shift away from the lattice tops is a good way [1]. However, based on the fundamental knowledge of "lattice", it often occurs that the tops of a lattice "should be" the positions of "atom balls" thought by most beginnings in teaching practice. This "thought" leads them never deduce out those regulations in symmetry operations and often misleads a wrong conclusion. As a beginning one wishes watching movies and pictures instead of mathematical deduction or vector calculation. It easily arises that a lattice has eight tops with atom balls. This "idea" lets the orientation balls shifting away from the lattice tops become difficult to understand. Nevertheless, the balls with a sign of "comma" in the middle are also difficult to understand that they can stand for a certain orientation because ball is circle. "Tops" and "directions" are two troubles in learning crystallographic symmetry and symmetry operations for those beginnings. How to guide them to overcome the two fences is an important step that will lead those beginnings to a never understanding status, on one hand, or let them understand throughout all regulations of space group(s) combining with a symmetry operation on the other. From teaching practice, a polyhedral at lattice tops could overcome both difficulties at position and in orientation. First, a polyhedral is always in orientation, even it is a cubic. This is easily understood. Secondly the centre of a polyhedral could easily meet with the tops of a lattice; it lets students easily understand "a lattice has eight tops occupied - a natural thought by beginnings". This way let them easily understand and deduce all regulations in crystallographic symmetry operations, such as a body-centred lattice combining with a symmetry plane (m) produces n symmetry operation at 1/4t, etc. see figures below.

Lattice row distance

Lattice and diffraction are two relating aspects of a crystal. The former reflects the nature of a crystal and the latter describes the basic feature of a crystal. A lattice possesses points and rows two basic characteristics. Great attention has been paid to the points and their distances and directions (angles) they form since the early time of crystallography. Starting from lattice points people have already revealed and found so many regulations in crystals and made great progresses in crystallography. What about the lattice rows? Starting from the geometric relations of reciprocal lattice, we propose six general formulae [1] to describe the relationships between the lattice row distance, the Miller indices h, k, l and the lattice parameters for all crystal systems along any direction. This, like the lattice points, establishes the foundation of the row-indexing, row-refinement of lattice parameters and row-determination of incidence direction theoretically. It is a new method from the lattice row distance to the Miller indices, to the lattice parameters or to the incidence direction. Five steps are optimized for the procedure of "Row-indexing" or "Row-refinement". For example, the procedure of row-indexing is described as 1) measurement of row distance; 2) calculation of row distance; 3) comparison of the measured with the calculated row distances; 4) indexing, and 5) check according to the crystallographic regulations. In respect to diffraction patterns, a series of diffraction spots (points) comprise row(s) and arrange into a series of parallel "lines". When diffraction is strong, diffraction spots are isolated and sharp. However, when diffraction is weak, those spots are obscure or gloomy and often distorted into elongation, asymmetry, deformation, etc. This leads to the outstanding of the rowing "lines" relatively and hence, the row-distance formulae are able to be utilized to structure analysis for those "linear diffraction patterns".