7TZD

Solution NMR of the specialized apo-acyl carrier protein (RPA2022) from Rhodopseudomonas palustris, refined without RDCs. Northeast Structural Genomics Consortium Target RpR324

7TZD の概要

• エントリーDOI: 10.2210/pdb7tzd/pdb
• NMR情報: BMRB: 18263
• 分子名称: Specialized acyl carrier protein (1 entity in total)
• 機能のキーワード: acp-xl, transferase, structural genomics, psi-biology, northeast structural genomics consortium, nesg
• 由来する生物種: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 11309.72

構造登録者

Ramelot, T.A.,Tejero, R.,Montelione, G.T.,Northeast Structural Genomics Consortium (NESG) (登録日: 2022-02-15, 公開日: 2022-08-10, 最終更新日: 2024-05-15)

主引用文献

Tejero, R.,Huang, Y.J.,Ramelot, T.A.,Montelione, G.T.
AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.
Front Mol Biosci, 9:877000-877000, 2022

PubMed Abstract: Recent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracies rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NMR and cryo-electron microscopy structures. Here we assess the hypothesis that AlphaFold models of small, relatively rigid proteins have accuracies (based on comparison against experimental data) similar to experimental solution NMR structures. We selected six representative small proteins with structures determined by both NMR and X-ray crystallography, and modeled each of them using AlphaFold. Using several structure validation tools integrated under the Protein Structure Validation Software suite (PSVS), we then assessed how well these models fit to experimental NMR data, including NOESY peak lists (RPF-DP scores), comparisons between predicted rigidity and chemical shift data (ANSURR scores), and N-H residual dipolar coupling data (RDC Q factors) analyzed by software tools integrated in the PSVS suite. Remarkably, the fits to NMR data for the protein structure models predicted with AlphaFold are generally similar, or better, than for the corresponding experimental NMR or X-ray crystal structures. Similar conclusions were reached in comparing AlphaFold2 predictions and NMR structures for three targets from the Critical Assessment of Protein Structure Prediction (CASP). These results contradict the widely held misperception that AlphaFold cannot accurately model solution NMR structures. They also document the value of PSVS for model vs. data assessment of protein NMR structures, and the potential for using AlphaFold models for guiding analysis of experimental NMR data and more generally in structural biology.

PubMed: 35769913
DOI: 10.3389/fmolb.2022.877000

実験手法

SOLUTION NMR