Summary: Fibrillarin
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Fibrillarin Edit Wikipedia article
| Fibrillarin | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 pyrococcus horikoshii fibrillarin pre-rrna processing protein | |||||||||
| Identifiers | |||||||||
| Symbol | Fibrillarin | ||||||||
| Pfam | PF01269 | ||||||||
| Pfam clan | CL0063 | ||||||||
| InterPro | IPR000692 | ||||||||
| PROSITE | PDOC00489 | ||||||||
| SCOPe | 1fbn / SUPFAM | ||||||||
| |||||||||
rRNA 2'-O-methyltransferase fibrillarin is an enzyme that in humans is encoded by the FBL gene.[5][6][7]
Function
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 nucleolar 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.[7]
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 archaea.
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.[8] 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.
Structural evidence supporting the idea that fibrillarin is the snoRNA methyltransferase has been reviewed.[9]
Interactions
Fibrillarin has been shown to interact with DDX5[10] and SMN1.[11]
References
- ^ a b c ENSG00000280548 GRCh38: Ensembl release 89: ENSG00000105202, ENSG00000280548 - Ensembl, May 2017
- ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000046865 - Ensembl, May 2017
- ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ Aris JP, Blobel G (Feb 1991). "cDNA cloning and sequencing of human fibrillarin, a conserved nucleolar protein recognized by autoimmune antisera". Proceedings of the National Academy of Sciences of the United States of America. 88 (3): 931–5. doi:10.1073/pnas.88.3.931. PMC 50928. PMID 1846968.
- ^ Jansen RP, Hurt EC, Kern H, Lehtonen H, Carmo-Fonseca M, Lapeyre B, Tollervey D (May 1991). "Evolutionary conservation of the human nucleolar protein fibrillarin and its functional expression in yeast". The Journal of Cell Biology. 113 (4): 715–29. doi:10.1083/jcb.113.4.715. PMC 2288999. PMID 2026646.
- ^ a b "Entrez Gene: FBL fibrillarin".
- ^ 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 SM, Causevic M, Prescott AR, Fuller-Pace FV (Jun 2000). "The nuclear DEAD box RNA helicase p68 interacts with the nucleolar protein fibrillarin and colocalizes specifically in nascent nucleoli during telophase". Experimental Cell Research. 257 (2): 272–80. doi:10.1006/excr.2000.4886. PMID 10837141.
- ^ Pellizzoni L, Baccon J, Charroux B, Dreyfuss G (Jul 2001). "The survival of motor neurons (SMN) protein interacts with the snoRNP proteins fibrillarin and GAR1". Current Biology. 11 (14): 1079–88. doi:10.1016/S0960-9822(01)00316-5. PMID 11509230.
Further reading
- Baserga SJ, Yang XD, Steitz JA (Sep 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". The EMBO Journal. 10 (9): 2645–51. doi:10.1002/j.1460-2075.1991.tb07807.x. PMC 452965. PMID 1714385.
- Okano Y, Steen VD, Medsger TA (Jan 1992). "Autoantibody to U3 nucleolar ribonucleoprotein (fibrillarin) in patients with systemic sclerosis". Arthritis and Rheumatism. 35 (1): 95–100. doi:10.1002/art.1780350114. PMID 1731817.
- Lischwe MA, Ochs RL, Reddy R, Cook RG, Yeoman LC, Tan EM, Reichlin M, Busch H (Nov 1985). "Purification and partial characterization of a nucleolar scleroderma antigen (Mr = 34,000; pI, 8.5) rich in NG,NG-dimethylarginine". The Journal of Biological Chemistry. 260 (26): 14304–10. PMID 2414294.
- Méhes G, Pajor L (Jun 1995). "Nucleolin and fibrillarin expression in stimulated lymphocytes and differentiating HL-60 cells. A flow cytometric assay". Cell Proliferation. 28 (6): 329–36. doi:10.1111/j.1365-2184.1995.tb00074.x. PMID 7626687.
- Liu Q, Dreyfuss G (Jul 1996). "A novel nuclear structure containing the survival of motor neurons protein". The EMBO Journal. 15 (14): 3555–65. doi:10.1002/j.1460-2075.1996.tb00725.x. PMC 451956. PMID 8670859.
- Magoulas C, Zatsepina OV, Jordan PW, Jordan EG, Fried M (Feb 1998). "The SURF-6 protein is a component of the nucleolar matrix and has a high binding capacity for nucleic acids in vitro". European Journal of Cell Biology. 75 (2): 174–83. doi:10.1016/s0171-9335(98)80059-9. PMID 9548374.
- Ai LS, Lin CH, Hsieh M, Li C (Oct 1999). "Arginine methylation of a glycine and arginine rich peptide derived from sequences of human FMRP and fibrillarin". Proceedings of the National Science Council, Republic of China. Part B, Life Sciences. 23 (4): 175–80. PMID 10518318.
- Pintard L, Kressler D, Lapeyre B (Feb 2000). "Spb1p is a yeast nucleolar protein associated with Nop1p and Nop58p that is able to bind S-adenosyl-L-methionine in vitro". Molecular and Cellular Biology. 20 (4): 1370–81. doi:10.1128/MCB.20.4.1370-1381.2000. PMC 85287. PMID 10648622.
- Nicol SM, Causevic M, Prescott AR, Fuller-Pace FV (Jun 2000). "The nuclear DEAD box RNA helicase p68 interacts with the nucleolar protein fibrillarin and colocalizes specifically in nascent nucleoli during telophase". Experimental Cell Research. 257 (2): 272–80. doi:10.1006/excr.2000.4886. PMID 10837141.
- Pellizzoni L, Baccon J, Charroux B, Dreyfuss G (Jul 2001). "The survival of motor neurons (SMN) protein interacts with the snoRNP proteins fibrillarin and GAR1". Current Biology. 11 (14): 1079–88. doi:10.1016/S0960-9822(01)00316-5. PMID 11509230.
- Zhou X, Tan FK, Xiong M, Milewicz DM, Feghali CA, Fritzler MJ, Reveille JD, Arnett FC (Dec 2001). "Systemic sclerosis (scleroderma): specific autoantigen genes are selectively overexpressed in scleroderma fibroblasts". Journal of Immunology. 167 (12): 7126–33. doi:10.4049/jimmunol.167.12.7126. PMID 11739535.
- Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI (Jan 2002). "Directed proteomic analysis of the human nucleolus". Current Biology. 12 (1): 1–11. doi:10.1016/S0960-9822(01)00650-9. PMID 11790298.
- Cimato TR, Tang J, Xu Y, Guarnaccia C, Herschman HR, Pongor S, Aletta JM (Feb 2002). "Nerve growth factor-mediated increases in protein methylation occur predominantly at type I arginine methylation sites and involve protein arginine methyltransferase 1". Journal of Neuroscience Research. 67 (4): 435–42. doi:10.1002/jnr.10123. PMID 11835310.
- Fujiyama S, Yanagida M, Hayano T, Miura Y, Isobe T, Fujimori F, Uchida T, Takahashi N (Jun 2002). "Isolation and proteomic characterization of human Parvulin-associating preribosomal ribonucleoprotein complexes". The Journal of Biological Chemistry. 277 (26): 23773–80. doi:10.1074/jbc.M201181200. PMID 11960984.
- Whitehead SE, Jones KW, Zhang X, Cheng X, Terns RM, Terns MP (Dec 2002). "Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1". The Journal of Biological Chemistry. 277 (50): 48087–93. doi:10.1074/jbc.M204551200. PMID 12244096.
- Herrera-Esparza R, Kruse L, von Essen M, Campos L, Barbosa O, Bollain JJ, Badillo I, Avalos-DÃaz E (Oct 2002). "U3 snoRNP associates with fibrillarin a component of the scleroderma clumpy nucleolar domain". Archives of Dermatological Research. 294 (7): 310–7. doi:10.1007/s00403-002-0338-7. PMID 12373336.
- Chen M, Rockel T, Steinweger G, Hemmerich P, Risch J, von Mikecz A (Oct 2002). "Subcellular recruitment of fibrillarin to nucleoplasmic proteasomes: implications for processing of a nucleolar autoantigen". Molecular Biology of the Cell. 13 (10): 3576–87. doi:10.1091/mbc.02-05-0083. PMC 129967. PMID 12388758.
- Watkins NJ, Dickmanns A, Lührmann R (Dec 2002). "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". Molecular and Cellular Biology. 22 (23): 8342–52. doi:10.1128/MCB.22.23.8342-8352.2002. PMC 134055. PMID 12417735.
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This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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
No Pfam abstract.
Internal database links
| SCOOP: | CMAS DREV FtsJ GCD14 GidB Met_10 Methyltr_RsmB-F Methyltransf_11 Methyltransf_12 Methyltransf_18 Methyltransf_2 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_3 Methyltransf_31 Methyltransf_32 Methyltransf_4 Methyltransf_9 MetW MTS PCMT PrmA RrnaAD TehB Ubie_methyltran |
| Similarity to PfamA using HHSearch: | PCMT FtsJ Methyltransf_11 Methyltransf_12 GCD14 Methyltransf_24 Methyltransf_25 Methyltransf_31 |
External database links
| PROSITE: | PDOC00489 |
| SCOP: | 1fbn |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000692
Fibrillarin 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.
Gene Ontology
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) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan NADP_Rossmann (CL0063), which has the following description:
A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.
The clan contains the following 206 members:
2-Hacid_dh_C 3Beta_HSD 3HCDH_N 3HCDH_RFF adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa B12-binding Bac_GDH Bin3 Bmt2 CbiJ CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 CoV_ExoN CoV_Methyltr_2 DAO DapB_N DFP DNA_methylase DOT1 DRE2_N DREV DUF1442 DUF1611_N DUF166 DUF1776 DUF2431 DUF268 DUF2855 DUF3410 DUF364 DUF43 DUF5129 DUF5130 DUF6094 DUF938 DXP_reductoisom DXPR_C Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ fvmX7 G6PD_N GCD14 GDI GDP_Man_Dehyd GFO_IDH_MocA GIDA GidB GLF Glu_dehyd_C Glyco_hydro_4 Glyco_tran_WecG GMC_oxred_N Gp_dh_N GRAS GRDA HcgC HI0933_like HIM1 IlvN ISPD_C K_oxygenase KR LCM Ldh_1_N LpxI_N Lycopene_cycl Malic_M Mannitol_dh MCRA Met_10 Methyltr_RsmB-F Methyltr_RsmF_N Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_14 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_33 Methyltransf_34 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C MOLO1 Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS OCD_Mu_crystall Orbi_VP4 PALP PARP_regulatory PCMT PDH PglD_N Polysacc_syn_2C Polysacc_synt_2 Pox_MCEL Pox_mRNA-cap Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 Reovirus_L2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Sacchrp_dh_NADP SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth TehB THF_DHG_CYH_C Thi4 ThiF TPM_phosphatase TPMT TrkA_N TRM TRM13 TrmK tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 Urocanase V_cholerae_RfbT XdhC_C YjeF_NAlignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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| Seed (34) |
Full (2403) |
Representative proteomes | UniProt (5974) |
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|---|---|---|---|---|---|---|---|
| RP15 (518) |
RP35 (1223) |
RP55 (1981) |
RP75 (2714) |
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| PP/heatmap | 1 | ||||||
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| Seed (34) |
Full (2403) |
Representative proteomes | UniProt (5974) |
||||
|---|---|---|---|---|---|---|---|
| RP15 (518) |
RP35 (1223) |
RP55 (1981) |
RP75 (2714) |
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| Raw Stockholm | |||||||
| Gzipped | |||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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'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.
Note: You can also download the data file for the tree.
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: | Prosite |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Finn RD  , Bateman A
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| Number in seed: | 34 |
| Number in full: | 2403 |
| Average length of the domain: | 201.10 aa |
| Average identity of full alignment: | 60 % |
| Average coverage of the sequence by the domain: | 69.45 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 226 | ||||||||||||
| Family (HMM) version: | 19 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Unclassified
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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 Fibrillarin domain has been found. There are 85 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 sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
| Protein | Predicted structure | External Information |
|---|---|---|
| A0A0N7KGC5 | View 3D Structure | Click here |
| A0A1D6DTS8 | View 3D Structure | Click here |
| A0A1D6GJM8 | View 3D Structure | Click here |
| A0A1D6GTM1 | View 3D Structure | Click here |
| A0A1D6LQV3 | View 3D Structure | Click here |
| A0A1D6LXF5 | View 3D Structure | Click here |
| A0A1D6NHU2 | View 3D Structure | Click here |
| A0A1D6PVT0 | View 3D Structure | Click here |
| A0A1D6PVT1 | View 3D Structure | Click here |
| A0A1D6Q1Z6 | View 3D Structure | Click here |
| A0A1D6Q8K2 | View 3D Structure | Click here |
| A0A1D6QAN9 | View 3D Structure | Click here |
| A0A1D6QPX4 | View 3D Structure | Click here |
| A4ID95 | View 3D Structure | Click here |
| A6NHQ2 | View 3D Structure | Click here |
| B7FA85 | View 3D Structure | Click here |
| D3ZVA5 | View 3D Structure | Click here |
| E9AGR2 | View 3D Structure | Click here |
| I1JXQ3 | View 3D Structure | Click here |
| I1MYV4 | View 3D Structure | Click here |
| K7KVG4 | View 3D Structure | Click here |
| K7LRU2 | View 3D Structure | Click here |
| P15646 | View 3D Structure | Click here |
| P22087 | View 3D Structure | Click here |
| P22509 | View 3D Structure | Click here |
| P35550 | View 3D Structure | Click here |
| P35551 | View 3D Structure | Click here |
| Q22053 | View 3D Structure | Click here |
| Q4DGF1 | View 3D Structure | Click here |
| Q4DIZ5 | View 3D Structure | Click here |
| Q4DYJ3 | View 3D Structure | Click here |
| Q4DZU7 | View 3D Structure | Click here |
| Q55CW0 | View 3D Structure | Click here |
| Q58108 | View 3D Structure | Click here |
| Q5A0V9 | View 3D Structure | Click here |
| Q7ZTZ4 | View 3D Structure | Click here |
| Q80WS3 | View 3D Structure | Click here |
| Q8IM23 | View 3D Structure | Click here |
| Q94AH9 | View 3D Structure | Click here |
| Q9FEF8 | View 3D Structure | Click here |
| Q9FHB3 | View 3D Structure | Click here |
| Q9VG21 | View 3D Structure | Click here |
| Q9W1V3 | View 3D Structure | Click here |
