PROSITE documentation PDOC51214
IBB domain profile


Cytosolic proteins bearing a classical nuclear localization signal (NLS) (see <PDOC00015>) enter the nucleus bound to a heterodimer of importin-α and importin-β (also called karyopherin-α and -β). Importin-α contains the NLS-binding site and importin-β is responsible for the docking of the importin-substrate complex to the filaments of the nuclear pore complex (NPC) and its translocation through the pore. Importin-α consists of two functional domains, a highly basic amino-terminal region of roughly 40 amino-acid residues (the IBB domain) responsible for importin-β binding, and an NLS-binding domain built of armadillo (ARM) repeats (see <PDOC50176>). Appart from the classical protein-import pathway, importin-β is also involved in the nuclear import of spliceosomal small nuclear ribonucleoprotein particles (snRNPs), which is mediated by the 45K protein snurportin-1. Snurportin-1 is functionally analogous to importin-α, as it recognizes the trimethylguanosine (m3G) cap structure of the small nuclear RNAs U1, U2, U4 and U5, and binds to importin-β through an IBB-domain. Snurportin-1 contains an N-terminal IBB domain and a C-terminal m3G-cap-binding region with no structural similarity to the arm repeat domain of importin-α [1,2,3].

The IBB domain is an L-shapped molecule with an N-terminal extended moiety and a C-terminal helix running in mutually perpendicular directions (see <PDB:1QGK>). The IBB domain is intimately bound on the inner surface of importin-β that contains many acidic residues and is thus complementary to the highly positively charged IBB domain [1,2].

The profile we developed covers the entire IBB domain.

Last update:

June 2006 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

IBB, PS51214; IBB domain profile  (MATRIX)


1AuthorsKobe B.
TitleAutoinhibition by an internal nuclear localization signal revealed by the crystal structure of mammalian importin alpha.
SourceNat. Struct. Biol. 6:388-397(1999).
PubMed ID10201409

2AuthorsCingolani G. Petosa C. Weis K. Mueller C.W.
TitleStructure of importin-beta bound to the IBB domain of importin-alpha.
SourceNature 399:221-229(1999).
PubMed ID10353244

3AuthorsHuber J. Cronshagen U. Kadokura M. Marshallsay C. Wada T. Sekine M. Luehrmann R.
TitleSnurportin1, an m3G-cap-specific nuclear import receptor with a novel domain structure.
SourceEMBO J. 17:4114-4126(1998).
PubMed ID9670026

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