2PEA

NMR Based Structure of the Closed Conformation of LYS48-Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements

Summary for 2PEA

• Entry DOI: 10.2210/pdb2pea/pdb
• Related: 1AAR 1D3Z 2BGF 2PE9
• Descriptor: Ubiquitin (1 entity in total)
• Functional Keywords: ubiquitin, lys48-linked di-ubiquitin, polyubiquitin, signaling protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 17153.66

Authors

Ryabov, Y.,Fushman, D. (deposition date: 2007-04-02, release date: 2007-07-10, Last modification date: 2024-05-22)

Primary citation

Ryabov, Y.,Fushman, D.
Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.
J.Am.Chem.Soc., 129:7894-7902, 2007

PubMed Abstract: We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein's rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning are also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of a Lys48-linked diubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution.

PubMed: 17550252
DOI: 10.1021/ja071185d

Experimental method

SOLUTION NMR