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3siv

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3siv, resolution 3.30Å ()
Gene: NHP2L1 (Homo sapiens), PRP31, PRPF31 (Homo sapiens)
Related: 2ozb, 3siu


Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, dimeric form

Publication Abstract from PubMed

Human proteins 15.5K and hPrp31 are components of the major spliceosomal U4 snRNP and of the minor spliceosomal U4atac snRNP. The two proteins bind to related 5'-stem loops (5'SLs) of the U4 and U4atac snRNAs in a strictly sequential fashion. The primary binding 15.5K protein binds at K-turns that exhibit identical sequences in the two snRNAs. However, RNA sequences contacted by the secondary binding hPrp31 differ in U4 and U4atac snRNAs, and the mechanism by which hPrp31 achieves its dual specificity is presently unknown. We show by crystal structure analysis that the capping pentaloops of the U4 and U4atac 5'SLs adopt different structures in the ternary hPrp31-15.5K-snRNA complexes. In U4atac snRNA, a noncanonical base pair forms across the pentaloop, based on which the RNA establishes more intimate interactions with hPrp31 compared with U4 snRNA. Stacking of hPrp31-His270 on the noncanonical base pair at the base of the U4atac pentaloop recapitulates intramolecular stabilizing principles known from the UUCG and GNRA families of RNA tetraloops. Rational mutagenesis corroborated the importance of the noncanonical base pair and the U4atac-specific hPrp31-RNA interactions for complex stability. The more extensive hPrp31-U4atac snRNA interactions are in line with a higher stability of the U4atac compared with the U4-based ternary complex seen in gel-shift assays, which may explain how U4atac snRNA can compete with the more abundant U4 snRNA for the same protein partners in vivo.

Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31., Liu S, Ghalei H, Luhrmann R, Wahl MC, RNA. 2011 Jul 22. PMID:21784869

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Disease

[PRP31_HUMAN] Defects in PRPF31 are the cause of retinitis pigmentosa type 11 (RP11) [MIM:600138]. RP leads to degeneration of retinal photoreceptor cells. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP11 inheritance is autosomal dominant.[1][2][3][4][5]

Function

[NH2L1_HUMAN] Binds to the 5'-stem-loop of U4 snRNA and may play a role in the late stage of spliceosome assembly. The protein undergoes a conformational change upon RNA-binding.[6][7] [PRP31_HUMAN] Involved in pre-mRNA splicing. Required for U4/U6.U5 tri-snRNP formation.[8]

About this Structure

3siv is a 12 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA.

See Also

Reference

  • Liu S, Ghalei H, Luhrmann R, Wahl MC. Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31. RNA. 2011 Jul 22. PMID:21784869 doi:10.1261/rna.2690611
  1. Liu S, Li P, Dybkov O, Nottrott S, Hartmuth K, Luhrmann R, Carlomagno T, Wahl MC. Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP. Science. 2007 Apr 6;316(5821):115-20. PMID:17412961 doi:316/5821/115
  2. Deery EC, Vithana EN, Newbold RJ, Gallon VA, Bhattacharya SS, Warren MJ, Hunt DM, Wilkie SE. Disease mechanism for retinitis pigmentosa (RP11) caused by mutations in the splicing factor gene PRPF31. Hum Mol Genet. 2002 Dec 1;11(25):3209-19. PMID:12444105
  3. Vithana EN, Abu-Safieh L, Allen MJ, Carey A, Papaioannou M, Chakarova C, Al-Maghtheh M, Ebenezer ND, Willis C, Moore AT, Bird AC, Hunt DM, Bhattacharya SS. A human homolog of yeast pre-mRNA splicing gene, PRP31, underlies autosomal dominant retinitis pigmentosa on chromosome 19q13.4 (RP11). Mol Cell. 2001 Aug;8(2):375-81. PMID:11545739
  4. Al-Maghtheh M, Vithana E, Tarttelin E, Jay M, Evans K, Moore T, Bhattacharya S, Inglehearn CF. Evidence for a major retinitis pigmentosa locus on 19q13.4 (RP11) and association with a unique bimodal expressivity phenotype. Am J Hum Genet. 1996 Oct;59(4):864-71. PMID:8808602
  5. Wang L, Ribaudo M, Zhao K, Yu N, Chen Q, Sun Q, Wang L, Wang Q. Novel deletion in the pre-mRNA splicing gene PRPF31 causes autosomal dominant retinitis pigmentosa in a large Chinese family. Am J Med Genet A. 2003 Sep 1;121A(3):235-9. PMID:12923864 doi:http://dx.doi.org/10.1002/ajmg.a.20224
  6. Nottrott S, Hartmuth K, Fabrizio P, Urlaub H, Vidovic I, Ficner R, Luhrmann R. Functional interaction of a novel 15.5kD [U4/U6.U5] tri-snRNP protein with the 5' stem-loop of U4 snRNA. EMBO J. 1999 Nov 1;18(21):6119-33. PMID:10545122 doi:10.1093/emboj/18.21.6119
  7. Liu S, Li P, Dybkov O, Nottrott S, Hartmuth K, Luhrmann R, Carlomagno T, Wahl MC. Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP. Science. 2007 Apr 6;316(5821):115-20. PMID:17412961 doi:316/5821/115
  8. Makarova OV, Makarov EM, Liu S, Vornlocher HP, Luhrmann R. Protein 61K, encoded by a gene (PRPF31) linked to autosomal dominant retinitis pigmentosa, is required for U4/U6*U5 tri-snRNP formation and pre-mRNA splicing. EMBO J. 2002 Mar 1;21(5):1148-57. PMID:11867543 doi:10.1093/emboj/21.5.1148

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