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There are currently at least 53 structures of components of nuclear transport in the Protein Databank. In addition to providing critical insights into molecular mechanisms of nuclear transport, these atomic resolution structures provide a large body of information that could guide biochemical and cell biological analyses involving nuclear transport proteins. This paper catalogs 53 crystal and NMR structures of nuclear transport proteins, with the emphasis on providing information useful for mutagenesis and overexpression of recombinant proteins.
High resolution structures of macromolecular complexes are necessary to understand molecular mechanisms of cellular processes. The importance of structures is particularly evident in the cellular process of nucleocytoplasmic transport. The nuclear transport machinery consists of a large number of proteins that include components of the nuclear pore complex (nucleoporins), transport factors that recognize import or export substrates (Karyopherins/Importins/Exportins and TAP), Ran, its transporter NTF2 and its regulators, RanBP1, RanGAP and RanGEF. Macromolecular interactions in nuclear transport are complex. Each protein generally contacts multiple macromolecular ligands, binding to different partners in the cytoplasm versus the nucleus. Partner-switching in the different subcellular compartments is also frequently accompanied with large conformational changes in the proteins. High resolution structures of nuclear transport complexes have been crucial in revealing how a transport factor recognizes its ligands and how structural plasticity plays a central role in the different steps of nuclear import and export.
High resolution structures that have been determined in nuclear transport include those of Kapβs, Kapαs, Ran and its regulators RanGAP, RanGEF, RanBP1 and NTF2, mRNA export factor TAP and nucleoporins. The list of Kapβ structures includes nine Kapβ1/Impβ structures (unliganded, Ran-, substrate- and nucleoporin-complexes), two Kapβ2/Transportin structures, two Cse1 structures and a structure of a small Crm1 fragment. A large number of Kapα structures are available, including nine of mouse Kapα and five of the yeast homolog Kap60p, providing insight into the recognition of a variety of classical-NLSs and also nucleoporins such as Nup50 and Nup2p. Ran, its regulators RanBP1, NTF2, RanGAP and RanGEF as well as complexes involving these proteins are also well represented with a total of 12 structures. Structures in mRNA export include eight structures of TAP or its yeast homolog Mex67p, and finally, there are currently five structures of individual nucleoporin domains.
Other than their important roles in revealing molecular mechanisms of cellular processes, high resolution structures of macromolecular complexes also provide tremendous resources and tools for biochemical and cell biological experimental design. Structures could provide critical guidance in mutagenesis studies, especially when the aim is to disrupt specific interactions. Structure determination efforts, which require large amounts of proteins also provide very useful information about overexpression and purification of recombinant proteins.
This paper strives to catalog a comprehensive list of high resolution structures (mostly crystal structures) in nuclear transport in Tables 1–6 and Figs. 1–6. We have tabulated information about the identity of successful protein constructs for each structure as well as residues that are observed in those structures, to guide production of recombinant proteins. Many proteins involved in nuclear transport contain multiple modular and globular domains (such as TAP and nucleoporins), and knowledge of where individual domains begin and end obtained from the structures will allow design of protein constructs to optimize both folding and function of those domains. In contrast to the common globular proteins, both Kapα and Kapβ proteins contain multiple HEAT/ARM repeats such that these proteins are either elongated or spiral-shape. More importantly, every single HEAT repeat helix in these proteins contributes to the extended hydrophobic cores of the proteins. Thus, it is not trivial to generate deletion mutants involving HEAT/ARM repeats without interfering with the folding or solubility of the proteins. Structures of karyopherin fragments summarized here should provide information on the few deletion mutants that have been overexpressed successfully. Many of the structures tabulated in this paper are those of complexes of two or more proteins. These structures are very informative as they reveal the chemical and physical nature of the contact interfaces. We have also included contact residues in individual binding partners seen in structures of complexes, and also information on published interface mutants that disrupt specific protein–protein interactions. Such structural and biochemical data should aid significantly in mutagenesis analysis especially to disrupt specific functions in this large group of proteins.
We have summarized 53 structures of Kapβs, Kapαs, Ran and its regulators RanGAP, RanGEF, RanBP1 and NTF2, mRNA export factor TAP and nucleoporins. The information provided should be useful for both overexpression of recombinant proteins as well as for analysis and experimental manipulation of specific interactions of the proteins. We look forward to many more structure of nuclear transport proteins in the future, especially to complexes of different Kapβs with their substrates to understand NLS/NES specificity in the different pathways and also to structures of nucleoporin subcomplexes to understand the assembly of the nuclear pore complex and mechanism of translocation through the pore.