2MJB
Solution nmr structure of ubiquitin refined against dipolar couplings in 4 media
Summary for 2MJB
| Entry DOI | 10.2210/pdb2mjb/pdb |
| Related | 1D3Z |
| Descriptor | Ubiquitin-60S ribosomal protein L40 (1 entity in total) |
| Functional Keywords | residual dipolar coupling, squalamine, signaling protein |
| Biological source | Homo sapiens (human) |
| Cellular location | Ubiquitin: Cytoplasm (By similarity). 60S ribosomal protein L40: Cytoplasm (By similarity): P62987 |
| Total number of polymer chains | 1 |
| Total formula weight | 8576.83 |
| Authors | Maltsev, A.,Grishaev, A.,Roche, J.,Zasloff, M.,Bax, A. (deposition date: 2014-01-02, release date: 2014-03-26, Last modification date: 2024-05-15) |
| Primary citation | 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 Cited by 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: 24568736DOI: 10.1021/ja4132642 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
Download full validation report
