Summary: XS domain
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The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 and SGS3 Q9LDX1. SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain has recently been predicted to possess an RRM-like RNA-binding domain  by fold recognition.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005380
The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X SWISSPROT and SGS3 SWISSPROT. SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important.
The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [PUBMED:12162795].
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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
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||12|
|Number in full:||211|
|Average length of the domain:||117.00 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||20.35 %|
|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:||9|
|Download:||download the raw HMM for this family|
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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 XS domain has been found. There are 2 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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