BioMagResBank News
May 23, 2022
NMRFAM Summer Workshop
NMRFAM (UW-Madison) and the CCRC NMR facility (University of Georgia) are excited to offer a hands-on workshop in solution NMR resonance assignment this summer. They are including some of the favorite parts of their prior workshops and updating the content with modern methods and applications to all kinds of proteins, structure validation, and mapping interactions. The workshop will be held in person the week of June 20 in Madison, WI. This workshop is part of NIH-supported research resource user training program and development of the NSF-supported Network for Advanced NMR. To register, go to the NMRFAM workshops page.
Workshop presenters include Katie Henzler-Wildman, Art Edison, Jim Prestegard, Marco Tonelli, Alex Eletsky and Vilius Kurauskas.
Content includes:
- The value of NMR in the modern era of structural biology – what can NMR bring to your research problem?
- Introduction to NAN, the Network for Advanced NMR, which seeks to make NMR more accessible to biomedical researchers and assist scientists in finding the NMR instruments and expertise needed to carry out their research projects.
- Hands-on practice with structure-based assignment of methyl groups. This can be used for:
- NMR validation of structural models in solution. This includes validation of alpha fold structures, homology models, and other computationally-derived models, as well as assessing whether the lowest energy state in solution is consistent with a crystal structure or cryoEM structure.
- Methyl assignment for further NMR studies. Methyl groups are sensitive probes for mapping interactions of proteins with other proteins, nucleic acids and small molecules. Methyl groups are also excellent probes for studying protein motion on a wide range of timescales.
- Sparse labeling and assignment strategies for NMR studies of glycoproteins and eukaryotic proteins. This is similar to methyl-labeling approaches, but opens up NMR studies of proteins that cannot be produced in bacteria. Hands-on practice with structure-based assignment approaches for these biomedically important systems.
- Standard backbone assignment process, the starting point for most NMR projects on small to medium sized proteins, including structure determination, analysis of protein dynamics, and mapping protein interactions.
- Chemical shift perturbations for assessing protein interactions with diverse binding partners. Approaches, pitfalls, assessing significance, and interpretation of data.
To learn more, please visit NMRFAM.
March 16, 2021
Modifications to support for SHEET and ligand SITE records in June 2021
In 2014, PDBx/mmCIF became the PDB’s archive format and the the legacy PDB file format was frozen. In addition to PDBx/mmCIF files for all entries, wwPDB produces PDB format-formatted files for entries that can be represented in this legacy file format (e.g., entries with over 99,999 atoms or with multi-character chain IDs are only available in PDBx/mmCIF)
As the size and complexity of PDB structures increases, additional limitations of the legacy PDB format are becoming apparent and need to be addressed.
Defining complex sheet records
Restrictions in the SHEET record fields in legacy the PDB file format do not allow for the generation of complex beta sheet topology. Complex beta sheet topologies include instances where beta strands are part of multiple beta sheets and other cases where the definition of the strands within a beta sheet cannot be presented in a linear description. For example, in PDB entry 5wln a large beta barrel structure is created from multiple copies of a single protein; within the beta sheet forming the barrel are instances of a single beta strand making contacts on one side with multiple other strands, even from different chains.
This limitation, however, is not an issue in the PDBx/mmCIF formatted file, where these complex beta sheet topology can be captured in _struct_sheet, _struct_sheet_order, _struct_sheet_range, and _struct_sheet_hbond.
Starting June 8th 2021, legacy PDB format files will no longer be generated for PDB entries where the SHEET topology cannot be generated. For these structures, wwPDB will continue to provide secondary structure information with helix and sheet information in the PDBx/mmCIF formatted file.
Deprecation of _struct_site (SITE) records
wwPDB regularly reviews the software used during OneDep biocuration. The _struct_site and _struct_site_gen categories in PDBx/mmCIF (SITE records in the legacy PDB file format) are generated by in-house software and based purely upon distance calculations, and therefore may not reflect biological functional sites.
Starting in June 2021, the in-house legacy software which produces _struct_site and _struct_site_gen records will be retired and wwPDB will no longer generate these categories for newly-deposited PDB entries. Existing entries will be unaffected.
