Summary: Nup53/35/40-type RNA recognition motif
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Nup53/35/40-type RNA recognition motif Provide feedback
Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane . This region of the Nup is the RNA-recognition region .
Handa N, Kukimoto-Niino M, Akasaka R, Kishishita S, Murayama K, Terada T, Inoue M, Kigawa T, Kose S, Imamoto N, Tanaka A, Hayashizaki Y, Shirouzu M, Yokoyama S;, J Mol Biol. 2006;363:114-124.: The crystal structure of mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain. PUBMED:16962612 EPMC:16962612
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This tab holds annotation information from the InterPro database.
InterPro entry IPR007846
The nuclear pore complex (NPC) mediates the transport of macromolecules across the nuclear envelope (NE). The NPC is composed of a relatively small number of proteins (~30), termed nucleoporins or Nups. The vertebrate nuclear pore protein Nup35, the ortholog of Saccharomyces cerevisiae Nup53p, is suggested to interact with the NE membrane and to be required for nuclear morphology. The highly conserved region between vertebrate Nup35 and yeast Nup53p is predicted to contain an RNA-recognition motif (RRM) domain.
The sequences of the RRM Nup-35-type domain are highly conserved in all eucaryotes. The RRM Nup35-type domain adopts the characteristic BetaAlphaBeta BetaAlphaBeta topology of the secondary structure elements, with a four- stranded antiparallel beta-sheet packed against two alpha helices. The RRM Nup35-type domain forms a homodimer and contains atypical rinonucleoprotein (RNP) motifs, which lack the conserved residues that typically bind RNA in canonical RRM domains. The dimer interface involves the beta-sheet surface, with its atypical RNP motifs, which is generally used to bind RNA in typical RRM domains [PUBMED:16962612].
This entry represents the RRM Nup35-type domain.
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This clan contains families that are related to the RNA recognition motif domains. However, not all these families are RNA binding.
The clan contains the following 15 members:BRAP2 Calcipressin DUF1866 Limkain-b1 Nup35_RRM Nup35_RRM_2 Ribosomal_L23 RNA_bind RRM_1 RRM_2 RRM_3 RRM_5 RRM_6 Smg4_UPF3 XS
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Curation and family details
|Seed source:||Guo JH|
|Author:||Guo JH, Coggill P|
|Number in seed:||7|
|Number in full:||252|
|Average length of the domain:||95.70 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||25.66 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Nup35_RRM domain has been found. There are 5 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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