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Fibrillarin Edit Wikipedia article
PDB rendering based on 2ipx.
|RNA expression pattern|
|pyrococcus horikoshii fibrillarin pre-rrna processing protein|
This gene product is a component of a nucleolar small nuclear ribonucleoprotein (snRNP) particle thought to participate in the first step in processing pre-ribosomal (r)RNA. It is associated with the U3, U8, and U13 small nuclear RNAs and is located in the dense fibrillar component (DFC) of the nucleolus. The encoded protein contains an N-terminal repetitive domain that is rich in glycine and arginine residues, like fibrillarins in other species. Its central region resembles an RNA-binding domain and contains an RNP consensus sequence. Antisera from approximately 8% of humans with the autoimmune disease scleroderma recognize fibrillarin.
Fibrillarin is a component of several ribonucleoproteins including a nucleolar small nuclear ribonucleoprotein (SnRNP) and one of the two classes of small nucleolar ribonucleoproteins (snoRNPs). SnRNAs function in RNA splicing while snoRNPs function in ribosomal RNA processing.
Fibrillarin is associated with U3, U8 and U13 small nuclear RNAs in mammals and is similar to the yeast NOP1 protein. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.
A study by Schultz et al. indicated that the K-turn binding 15.5-kDa protein (called Snu13 in yeast) interacts with spliceosome proteins hPRP31, hPRP3, hPRP4, CYPH and the small nucleolar ribonucleoproteins NOP56, NOP58, and fibrillarin. The 15.5-kDa protein has sequence similarity to other RNA-binding proteins such as ribosomal proteins S12, L7a, and L30 and the snoRNP protein NHP2. The U4/U6 snRNP contains 15.5-kDa protein. The 15.5-kDa protein also exists in a ribonucleoprotein complex that binds the U3 box B/C motif. The 15.5-kDa protein also exists as one of the four core proteins of the C/D small nucleolar ribonucleoprotein that mediates methylation of pre-ribosomal RNAs.
- Aris JP, Blobel G (March 1991). "cDNA cloning and sequencing of human fibrillarin, a conserved nucleolar protein recognized by autoimmune antisera". Proc Natl Acad Sci U S A 88 (3): 931–5. doi:10.1073/pnas.88.3.931. PMC 50928. PMID 1846968. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=50928.
- Jansen RP, Hurt EC, Kern H, Lehtonen H, Carmo-Fonseca M, Lapeyre B, Tollervey D (June 1991). "Evolutionary conservation of the human nucleolar protein fibrillarin and its functional expression in yeast". J Cell Biol 113 (4): 715–29. doi:10.1083/jcb.113.4.715. PMC 2288999. PMID 2026646. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2288999.
- "Entrez Gene: FBL fibrillarin". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2091.
- Protein-Protein and Protein-RNA Contacts both Contribute to the 15.5K-Mediated Assembly of the U4/U6 snRNP and the Box C/D snoRNPs by Annemarie Schultz, Stephanie Nottrott, Nicholas James Watkins and Reinhard Lührmann in Molecular and Cellular Biology (2006) Volume 26, pages 5146–5154.
- The structure and function of small nucleolar ribonucleoproteins by Steve L. Reichow, Tomoko Hamma, Adrian R. Ferré-D'Amaré and Gabriele Varani in Nucleic Acids Research (2007) Volume 35, pages 1452–1464.
- Nicol, S M; Causevic M, Prescott A R, Fuller-Pace F V (June 2000). "The nuclear DEAD box RNA helicase p68 interacts with the nucleolar protein fibrillarin and colocalizes specifically in nascent nucleoli during telophase". Exp. Cell Res. (UNITED STATES) 257 (2): 272–80. doi:10.1006/excr.2000.4886. ISSN 0014-4827. PMID 10837141.
- Pellizzoni, L; Baccon J, Charroux B, Dreyfuss G (July 2001). "The survival of motor neurons (SMN) protein interacts with the snoRNP proteins fibrillarin and GAR1". Curr. Biol. (England) 11 (14): 1079–88. doi:10.1016/S0960-9822(01)00316-5. ISSN 0960-9822. PMID 11509230.
 Further reading
- Baserga SJ, Yang XD, Steitz JA (1991). "An intact Box C sequence in the U3 snRNA is required for binding of fibrillarin, the protein common to the major family of nucleolar snRNPs". EMBO J. 10 (9): 2645–51. PMC 452965. PMID 1714385. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=452965.
- Okano Y, Steen VD, Medsger TA (1992). "Autoantibody to U3 nucleolar ribonucleoprotein (fibrillarin) in patients with systemic sclerosis". Arthritis Rheum. 35 (1): 95–100. doi:10.1002/art.1780350114. PMID 1731817.
- Lischwe MA, Ochs RL, Reddy R et al (1985). "Purification and partial characterization of a nucleolar scleroderma antigen (Mr = 34,000; pI, 8.5) rich in NG,NG-dimethylarginine". J. Biol. Chem. 260 (26): 14304–10. PMID 2414294.
- Méhes G, Pajor L (1995). "Nucleolin and fibrillarin expression in stimulated lymphocytes and differentiating HL-60 cells. A flow cytometric assay". Cell Prolif. 28 (6): 329–36. doi:10.1111/j.1365-2184.1995.tb00074.x. PMID 7626687.
- Liu Q, Dreyfuss G (1996). "A novel nuclear structure containing the survival of motor neurons protein". EMBO J. 15 (14): 3555–65. PMC 451956. PMID 8670859. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=451956.
- Magoulas C, Zatsepina OV, Jordan PW et al (1998). "The SURF-6 protein is a component of the nucleolar matrix and has a high binding capacity for nucleic acids in vitro". Eur. J. Cell Biol. 75 (2): 174–83. PMID 9548374.
- Ai LS, Lin CH, Hsieh M, Li C (1999). "Arginine methylation of a glycine and arginine rich peptide derived from sequences of human FMRP and fibrillarin". Proc. Natl. Sci. Counc. Repub. China B 23 (4): 175–80. PMID 10518318.
- Pintard L, Kressler D, Lapeyre B (2000). "Spb1p Is a Yeast Nucleolar Protein Associated with Nop1p and Nop58p That Is Able To Bind S-Adenosyl-l-Methionine In Vitro". Mol. Cell. Biol. 20 (4): 1370–81. doi:10.1128/MCB.20.4.1370-1381.2000. PMC 85287. PMID 10648622. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=85287.
- Nicol SM, Causevic M, Prescott AR, Fuller-Pace FV (2000). "The nuclear DEAD box RNA helicase p68 interacts with the nucleolar protein fibrillarin and colocalizes specifically in nascent nucleoli during telophase". Exp. Cell Res. 257 (2): 272–80. doi:10.1006/excr.2000.4886. PMID 10837141.
- Pellizzoni L, Baccon J, Charroux B, Dreyfuss G (2001). "The survival of motor neurons (SMN) protein interacts with the snoRNP proteins fibrillarin and GAR1". Curr. Biol. 11 (14): 1079–88. doi:10.1016/S0960-9822(01)00316-5. PMID 11509230.
- Zhou X, Tan FK, Xiong M et al (2001). "Systemic sclerosis (scleroderma): specific autoantigen genes are selectively overexpressed in scleroderma fibroblasts". J. Immunol. 167 (12): 7126–33. PMID 11739535.
- Andersen JS, Lyon CE, Fox AH et al (2002). "Directed proteomic analysis of the human nucleolus". Curr. Biol. 12 (1): 1–11. doi:10.1016/S0960-9822(01)00650-9. PMID 11790298.
- Cimato TR, Tang J, Xu Y et al (2002). "Nerve growth factor-mediated increases in protein methylation occur predominantly at type I arginine methylation sites and involve protein arginine methyltransferase 1". J. Neurosci. Res. 67 (4): 435–42. doi:10.1002/jnr.10123. PMID 11835310.
- Fujiyama S, Yanagida M, Hayano T et al (2002). "Isolation and proteomic characterization of human Parvulin-associating preribosomal ribonucleoprotein complexes". J. Biol. Chem. 277 (26): 23773–80. doi:10.1074/jbc.M201181200. PMID 11960984.
- Whitehead SE, Jones KW, Zhang X et al (2003). "Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1". J. Biol. Chem. 277 (50): 48087–93. doi:10.1074/jbc.M204551200. PMID 12244096.
- Herrera-Esparza R, Kruse L, von Essen M et al (2003). "U3 snoRNP associates with fibrillarin a component of the scleroderma clumpy nucleolar domain". Arch. Dermatol. Res. 294 (7): 310–7. doi:10.1007/s00403-002-0338-7. PMID 12373336.
- Chen M, Rockel T, Steinweger G et al (2003). "Subcellular Recruitment of Fibrillarin to Nucleoplasmic Proteasomes: Implications for Processing of a Nucleolar Autoantigen". Mol. Biol. Cell 13 (10): 3576–87. doi:10.1091/mbc.02-05-0083. PMC 129967. PMID 12388758. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=129967.
- Watkins NJ, Dickmanns A, Lührmann R (2003). "Conserved Stem II of the Box C/D Motif Is Essential for Nucleolar Localization and Is Required, Along with the 15.5K Protein, for the Hierarchical Assembly of the Box C/D snoRNP". Mol. Cell. Biol. 22 (23): 8342–52. doi:10.1128/MCB.22.23.8342-8352.2002. PMC 134055. PMID 12417735. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=134055.
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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Fibrillarin Provide feedback
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Internal database links
|Similarity to PfamA using HHSearch:||FtsJ PCMT Methyltransf_11 Methyltransf_12 Methyltransf_18 Methyltransf_24 Methyltransf_25 Methyltransf_26 Methyltransf_31|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000692Fibrillarin is a component of a nucleolar small nuclear ribonucleoprotein (SnRNP), functioning in vivo in ribosomal RNA processing [PUBMED:2026646, PUBMED:8493104]. It is associated with U3, U8 and U13 small nuclear RNAs in mammals [PUBMED:2026646] and is similar to the yeast NOP1 protein [PUBMED:2686980]. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||RNA binding (GO:0003723)|
|methyltransferase activity (GO:0008168)|
|Biological process||rRNA processing (GO:0006364)|
|tRNA processing (GO:0008033)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
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This page displays the phylogenetic tree for this family's seed alignment. 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 alignment.
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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.
|Author:||Finn RD, Bateman A|
|Number in seed:||42|
|Number in full:||616|
|Average length of the domain:||215.80 aa|
|Average identity of full alignment:||57 %|
|Average coverage of the sequence by the domain:||78.68 %|
|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:||12|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
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.
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.
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There are 2 interactions 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 Fibrillarin domain has been found. There are 19 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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