New restraints and validation approaches for nucleic acid structures in PDB-REDO.

Ida de Vries,Tim Kwakman,Anastassis Perrakis,Mandar Deshpande,Robbie P. Joosten,Sameer Velankar,Xiang-Jun Lu,Maarten L. Hekkelman

doi:10.1107/s2059798321007610

Abstract

The quality of macromolecular structure models crucially depends on refinement and validation targets, which optimally describe the expected chemistry. Commonly used software for these two procedures has been designed and developed in a protein-centric manner, resulting in relatively few established features for the refinement and validation of nucleic acid-containing structure models. Here, new nucleic acid-specific approaches implemented in PDB-REDO are described, including a new restraint model using noncovalent geometries (base-pair hydrogen bonding and base-pair stacking) as refinement targets. New validation routines are also presented, including a metric for Watson-Crick base-pair geometry normality (ZbpG). Applying the PDB-REDO pipeline with the new restraint model to the whole Protein Data Bank (PDB) demonstrates an overall positive effect on the quality of nucleic acid-containing structure models. Finally, we discuss examples of improvements in the geometry of specific nucleic acid structures in the PDB. The new PDB-REDO models and pipeline are available at https://pdb-redo.eu/.

Highlights

Refinement and validation are important steps in the process of obtaining reliable structure models of macromolecules from X-ray crystallographic experiments and cryo-electron microscopy
The number of nucleic acid-containing structure models in the Protein Data Bank (PDB; wwPDB Consortium, 2019) is increasing, notably due to the successes achieved in resolving large protein–nucleic acid complexes using cryoEM (Mitra, 2019)
The restraint and validation targets that we derived for hydrogen-bond lengths (Table 1) and the relative orientations of bases in WC base pairs (Table 2) differ significantly for different types of nucleic acids (DNA–DNA, RNA–RNA or DNA–RNA)

Summary

Introduction

Refinement and validation are important steps in the process of obtaining reliable structure models of macromolecules from X-ray crystallographic experiments and cryo-electron microscopy (cryo-EM). Parkinson and coworkers were the first to publish targets and tolerances for the covalent geometry of nucleic acid structures (Parkinson et al, 1996) These were implemented in many refinement programs (Brunger, 1992; Blanc et al, 2004; Sheldrick, 2008, 2015; Murshudov et al, 2011; Liebschner et al, 2019) and validation tools (Hooft et al, 1996; Chen et al, 2010; wwPDB Consortium, 2019). To remedy this issue, the developers of these tools are working together to come to new consensus targets for nucleic acid covalent geometry (Schneider et al, 2020). An important challenge in nucleic acid structure geometry optimization remains: the bond-length and bondangle parameters for the (deoxy)riboses and the phosphate depend on the local conformation of the nucleic acid (Kowiel et al, 2016, 2020)

Methods

Results

Conclusion