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2y9c, resolution 3.60Å ()
Gene: SNRPB (Homo sapiens), SNRPD1 (Homo sapiens), SNRPD2 (Homo sapiens), SNRPD3 (Homo sapiens), SNRPE (Homo sapiens), SNRPF (Homo sapiens), SNRPG (Homo sapiens), RNU4A (Homo sapiens)
Related: 2y9a, 2y9b, 2y9d, 1d3b, 1b34, 3cw1, 3pgw

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



Publication Abstract from PubMed

The spliceosome is a dynamic macromolecular machine that assembles on pre-messenger RNA substrates and catalyses the excision of non-coding intervening sequences (introns). Four of the five major components of the spliceosome, U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), contain seven Sm proteins (SmB/B', SmD1, SmD2, SmD3, SmE, SmF and SmG) in common. Following export of the U1, U2, U4 and U5 snRNAs to the cytoplasm, the seven Sm proteins, chaperoned by the survival of motor neurons (SMN) complex, assemble around a single-stranded, U-rich sequence called the Sm site in each small nuclear RNA (snRNA), to form the core domain of the respective snRNP particle. Core domain formation is a prerequisite for re-import into the nucleus, where these snRNPs mature via addition of their particle-specific proteins. Here we present a crystal structure of the U4 snRNP core domain at 3.6 A resolution, detailing how the Sm site heptad (AUUUUUG) binds inside the central hole of the heptameric ring of Sm proteins, interacting one-to-one with SmE-SmG-SmD3-SmB-SmD1-SmD2-SmF. An irregular backbone conformation of the Sm site sequence combined with the asymmetric structure of the heteromeric protein ring allows each base to interact in a distinct manner with four key residues at equivalent positions in the L3 and L5 loops of the Sm fold. A comparison of this structure with the U1 snRNP at 5.5 A resolution reveals snRNA-dependent structural changes outside the Sm fold, which may facilitate the binding of particle-specific proteins that are crucial to biogenesis of spliceosomal snRNPs.

Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis., Leung AK, Nagai K, Li J, Nature. 2011 Apr 24. PMID:21516107

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

About this Structure

2y9c is a 24 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA.

See Also


  • Leung AK, Nagai K, Li J. Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. Nature. 2011 Apr 24. PMID:21516107 doi:10.1038/nature09956
  • Kambach C, Walke S, Young R, Avis JM, de la Fortelle E, Raker VA, Luhrmann R, Li J, Nagai K. Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell. 1999 Feb 5;96(3):375-87. PMID:10025403
  • Toro I, Thore S, Mayer C, Basquin J, Seraphin B, Suck D. RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex. EMBO J. 2001 May 1;20(9):2293-303. PMID:11331594 doi:10.1093/emboj/20.9.2293
  • Pomeranz Krummel DA, Oubridge C, Leung AK, Li J, Nagai K. Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature. 2009 Mar 26;458(7237):475-80. PMID:19325628 doi:10.1038/nature07851
  • Weber G, Trowitzsch S, Kastner B, Luhrmann R, Wahl MC. Functional organization of the Sm core in the crystal structure of human U1 snRNP. EMBO J. 2010 Dec 15;29(24):4172-84. Epub 2010 Nov 26. PMID:21113136 doi:10.1038/emboj.2010.295

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