9qtj | pdb_00009qtj

Structure of Oceanobacillus iheyensis group II intron domains D1-D6

spinqualitylabelsall models 9qtj, resolution 3.79Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9qtj is a 1 chain structure with sequence from Oceanobacillus iheyensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Electron Microscopy, Resolution 3.79Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, for example, the nucleic-acid backbone bends, deviating from an A-form helix geometry, or a base forms a non-standard hydrogen bond (not a Watson-Crick base pair). These bends and non-canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community. Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.,Kretsch RC, Albrecht R, Andersen ES, Chen HA, Chiu W, Das R, Gezelle JG, Hartmann MD, Hobartner C, Hu Y, Jadhav S, Johnson PE, Jones CP, Koirala D, Kristoffersen EL, Largy E, Lewicka A, Mackereth CD, Marcia M, Nigro M, Ojha M, Piccirilli JA, Rice PA, Shin H, Steckelberg AL, Su Z, Srivastava Y, Wang L, Wu Y, Xie J, Zwergius NH, Moult J, Kryshtafovych A Proteins. 2026 Jan;94(1):51-78. doi: 10.1002/prot.70043. Epub 2025 Sep 4. PMID:40905273 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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