2MJB

Solution nmr structure of ubiquitin refined against dipolar couplings in 4 media

2MJB の概要

• エントリーDOI: 10.2210/pdb2mjb/pdb
• 関連するPDBエントリー: 1D3Z
• 分子名称: Ubiquitin-60S ribosomal protein L40 (1 entity in total)
• 機能のキーワード: residual dipolar coupling, squalamine, signaling protein
• 由来する生物種: Homo sapiens (human)
• 細胞内の位置: Ubiquitin: Cytoplasm (By similarity). 60S ribosomal protein L40: Cytoplasm (By similarity): P62987
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 8576.83

構造登録者

Maltsev, A.,Grishaev, A.,Roche, J.,Zasloff, M.,Bax, A. (登録日: 2014-01-02, 公開日: 2014-03-26, 最終更新日: 2024-05-15)

主引用文献

Maltsev, A.S.,Grishaev, A.,Roche, J.,Zasloff, M.,Bax, A.
Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.
J.Am.Chem.Soc., 136:3752-3755, 2014

PubMed Abstract: The antibiotic squalamine forms a lyotropic liquid crystal at very low concentrations in water (0.3-3.5% w/v), which remains stable over a wide range of temperature (1-40 °C) and pH (4-8). Squalamine is positively charged, and comparison of the alignment of ubiquitin relative to 36 previously reported alignment conditions shows that it differs substantially from most of these, but is closest to liquid crystalline cetyl pyridinium bromide. High precision residual dipolar couplings (RDCs) measured for the backbone (1)H-(15)N, (15)N-(13)C', (1)H(α)-(13)C(α), and (13)C'-(13)C(α) one-bond interactions in the squalamine medium fit well to the static structural model previously derived from NMR data. Inclusion into the structure refinement procedure of these RDCs, together with (1)H-(15)N and (1)H(α)-(13)C(α) RDCs newly measured in Pf1, results in improved agreement between alignment-induced changes in (13)C' chemical shift, (3)JHNHα values, and (13)C(α)-(13)C(β) RDCs and corresponding values predicted by the structure, thereby validating the high quality of the single-conformer structural model. This result indicates that fitting of a single model to experimental data provides a better description of the average conformation than does averaging over previously reported NMR-derived ensemble representations. The latter can capture dynamic aspects of a protein, thus making the two representations valuable complements to one another.

PubMed: 24568736
DOI: 10.1021/ja4132642

実験手法

SOLUTION NMR