Summary

Importin beta binding domain

This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain [4].

Literature references

Conti E, Uy M, Leighton L, Blobel G, Kuriyan J; , Cell 1998;94:193-204.: Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. PUBMED:9695948
Weis K; , Trends Biochem Sci 1998;23:185-189.: Importins and exportins: how to get in and out of the nucleus [published erratum appears in Trends Biochem Sci 1998 Jul;23(7):235] PUBMED:9612083
Gorlich D; , EMBO J 1998;17:2721-2727.: Transport into and out of the cell nucleus. PUBMED:9582265
Moroianu J, Blobel G, Radu A; , Proc Natl Acad Sci U S A 1996;93:6572-6576.: The binding site of karyopherin alpha for karyopherin beta overlaps with a nuclear localization sequence. PUBMED:8692858
Gorlich D, Henklein P, Laskey RA, Hartmann E; , EMBO J 1996;15:1810-1817.: A 41 amino acid motif in importin-alpha confers binding to importin- beta and hence transit into the nucleus. PUBMED:8617226

InterPro entry IPR002652

The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments.

Members of the importin-alpha (karyopherin-alpha) family can form heterodimers with importin-beta. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Proteins can contain one (monopartite) or two (bipartite) NLS motifs. Importin-alpha contains several armadillo (ARM) repeats, which produce a curving structure with two NLS-binding sites, a major one close to the N-terminus and a minor one close to the C-terminus.

Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. The N-terminal importin-beta-binding (IBB) domain of importin-alpha contains an auto-regulatory region that mimics the NLS motif PUBMED:8692858. The release of importin-beta frees the auto-regulatory region on importin-alpha to loop back and bind to the major NLS-binding site, causing the cargo to be released PUBMED:17170104.

This entry represents the N-terminal IBB domain of importin-alpha that contains the auto-regulatory region.

More information about these proteins can be found at Protein of the Month: Importins PUBMED:.

Clan

This family is a member of clan TPR (CL0020), which contains the following 67 members:

Adaptin_N Arm Avirulence BTAD ChAPs CLASP_N Clathrin Clathrin-link Clathrin_propel Coatomer_E Cohesin_load CRM1_C Cse1 DNA_alkylation Drf_FH3 Drf_GBD DUF2225 DUF634 DUF654 FAT GUN4 HAT HEAT HEAT_PBS HemY_N IBB IBN_N IFRD IML2 KAP Leuk-A4-hydro_C LRV LRV_FeS MA3 MIF4G MIF4G_like MIF4G_like_2 Mo25 Neurochondrin NSF Paf67 ParcG PC_rep PHAT PI3Ka PPR Proteasom_PSMB PUF Rapsyn_N RPN7 Sel1 SHNi-TPR SPO22 ST7 Suf SusD TOM20_plant TPR_1 TPR_2 TPR_3 TPR_4 Upf2 V-ATPase_H_C V-ATPase_H_N Vps39_1 W2 Xpo1

Gene Ontology

Cellular component	nuclear pore (GO:0005643)
	nucleus (GO:0005634)
	cytoplasm (GO:0005737)
Molecular function	protein transporter activity (GO:0008565)
Biological process	intracellular protein transport (GO:0006886)
Biological process	protein import into nucleus (GO:0006606)

External database links

HOMSTRAD:	ARM
PANDIT:	PF01749
SCOP:	1bk5
SYSTERS:	IBB

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Alignment:	Seed (18) Full (355) NCBI (547) Metagenomics (4)
Viewer:

Formatting options

Alignment:	Seed (18) Full (355)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (18) Full (355) NCBI (547) Metagenomics (4)
Full length sequences	Full-sequences (355)

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER2.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Pfam-B_544 (release 4.2)

Previous IDs:

none

Type:

Family

Author:

Bashton M, Bateman A

Number in seed:

18

Number in full:

355

Average length of the domain:

93.40 aa

Average identity of full alignment:

30 %

Average coverage of the sequence by the domain:

18.52 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	23.6	23.6
Trusted cut-off	23.9	24.0
Noise cut-off	23.5	23.5

Model length:

97

Family (HMM) version:

13

Download:

download the raw HMM for this family

Species distribution

Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the IBB domain has been found.

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Family: IBB (PF01749)

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