Analysis and validation of overall N-glycan conformation in Privateer.

The oligosaccharides in N-glycosylation provide key structural and functional contributions to a glycoprotein. These contributions are dependent on the composition and overall conformation of the glycans. The Privateer software allows structural biologists to evaluate and improve the atomic structures of carbohydrates, including N-glycans; this software has recently been extended to check glycan composition through the use of glycomics data. Here, a broadening of the scope of the software to analyse and validate the overall conformation of N-glycans is presented, focusing on a newly compiled set of glycosidic linkage torsional preferences harvested from a curated set of glycoprotein models.

The CCP4 suite: integrative software for macromolecular crystallography.

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

Updated restraint dictionaries for carbohydrates in the pyranose form.

Restraint dictionaries are used during macromolecular structure refinement to encapsulate intramolecular connectivity and geometric information. These dictionaries allow previously determined `ideal' values of features such as bond lengths, angles and torsions to be used as restraint targets. During refinement, restraints influence the model to adopt a conformation that agrees with prior observation. This is especially important when refining crystal structures of glycosylated proteins, as their resolutions tend to be worse than those of nonglycosylated proteins. Pyranosides, the overwhelming majority component in all forms of protein glycosylation, often display conformational errors in crystal structures. Whilst many of these flaws usually relate to model building, refinement issues may also have their root in suboptimal restraint dictionaries. In order to avoid subsequent misinterpretation and to improve the quality of all pyranose monosaccharide entries in the CCP4 Monomer Library, new dictionaries with improved ring torsion restraints, coordinates reflecting the lowest-energy ring pucker and updated geometry have been produced and evaluated. These new dictionaries are now part of the CCP4 Monomer Library and will be released with CCP4 version 8.0.

Structural glycobiology in the age of electron cryo-microscopy.

The methodology underpinning the construction, refinement, validation and analysis of atomic models of glycoproteins and protein-carbohydrate complexes has received a long-overdue boost in the last five years. This is a very timely development, as the resolution revolution in electron cryo-microscopy is now routinely delivering structures of key glycomedical importance, with a three-dimensional precision where X-ray crystallographic methods have traditionally floundered. This review will focus on the new software developments that have been introduced in the past two years, and their impact on the field of structural glycobiology in terms of published structures.