PDBsum entry 1u2f

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protein links
RNA-binding protein PDB id
Protein chain
90 a.a. *
* Residue conservation analysis
PDB id:
Name: RNA-binding protein
Title: Solution structure of the first RNA-binding domain of hu2af65
Structure: Protein (splicing factor u2af 65 kd subunit). Chain: a. Fragment: first RNA-binding domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21 (de3).
NMR struc: 1 models
Authors: T.Ito,Y.Muto,M.R.Green,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
T.Ito et al. (1999). Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)). EMBO J, 18, 4523-4534. PubMed id: 10449418 DOI: 10.1093/emboj/18.16.4523
26-May-99     Release date:   20-Aug-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P26368  (U2AF2_HUMAN) -  Splicing factor U2AF 65 kDa subunit
475 a.a.
90 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     2 terms  


DOI no: 10.1093/emboj/18.16.4523 EMBO J 18:4523-4534 (1999)
PubMed id: 10449418  
Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)).
T.Ito, Y.Muto, M.R.Green, S.Yokoyama.
The large subunit of the human U2 small nuclear ribonucleoprotein particle auxiliary factor (hU2AF(65)) is an essential RNA-splicing factor required for the recognition of the polypyrimidine tract immediately upstream of the 3' splice site. In the present study, we determined the solution structures of two hU2AF(65) fragments, corresponding to the first and second RNA-binding domains (RBD1 and RBD2, respectively), by nuclear magnetic resonance spectroscopy. The tertiary structure of RBD2 is similar to that of typical RNA-binding domains with the beta1-alpha1-beta2-beta3-alpha2-beta4 topology. In contrast, the hU2AF(65) RBD1 structure has unique features: (i) the alpha1 helix is elongated by one turn toward the C-terminus; (ii) the loop between alpha1 and beta2 (the alpha1/beta2 loop) is much longer and has a defined conformation; (iii) the beta2 strand is (188)AVQIN(192), which was not predicted by sequence alignments; and (iv) the beta2/beta3 loop is much shorter. Chemical shift perturbation experiments showed that the U2AF-binding RNA fragments interact with the four beta-strands of RBD2 whereas, in contrast, they interact with beta1, beta3 and beta4, but not with beta2 or the alpha1/beta2 loop, of RBD1. The characteristic alpha1-beta2 structure of the hU2AF(65) RBD1 may interact with other proteins, such as UAP56.
  Selected figure(s)  
Figure 1.
Figure 1 A schematic diagram of the domain structure of hU2AF^65. The RS domain refers to the arginine/serine-rich domain, and RBD stands for an RNA-binding domain. The arrows indicate the N- and C-terminal positions of the polypeptides used in this study.
Figure 8.
Figure 8 Possible base-binding positions of the hU2AF^65 RBD1 and RBD2. The amino acid residues that might stack with bases in the first, second and third canonical base-binding sites are shown, colored in magenta, green and cyan, respectively. On each binding site, a schematic pyrimidine base and a N1–C1' bond are presented.
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 4523-4534) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21753750 C.D.Mackereth, T.Madl, S.Bonnal, B.Simon, K.Zanier, A.Gasch, V.Rybin, J.Valcárcel, and M.Sattler (2011).
Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF.
  Nature, 475, 408-411.
PDB codes: 2yh0 2yh1
18987886 Q.Zhang, J.Li, Q.Li, X.Li, Z.Liu, D.Song, and Z.Xie (2009).
Cloning and characterization of the gene encoding the bovine BOULE protein.
  Mol Genet Genomics, 281, 67-75.  
19000813 J.Sperling, M.Azubel, and R.Sperling (2008).
Structure and function of the Pre-mRNA splicing machine.
  Structure, 16, 1605-1615.  
17188295 K.R.Thickman, E.A.Sickmier, and C.L.Kielkopf (2007).
Alternative conformations at the RNA-binding surface of the N-terminal U2AF(65) RNA recognition motif.
  J Mol Biol, 366, 703-710.
PDB code: 2hzc
  16682775 E.A.Sickmier, K.E.Frato, and C.L.Kielkopf (2006).
Crystallization and preliminary X-ray analysis of a U2AF65 variant in complex with a polypyrimidine-tract analogue by use of protein engineering.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 457-459.  
16818232 E.A.Sickmier, K.E.Frato, H.Shen, S.R.Paranawithana, M.R.Green, and C.L.Kielkopf (2006).
Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65.
  Mol Cell, 23, 49-59.
PDB codes: 2fzr 2g4b
16075426 C.D.Mackereth, B.Simon, and M.Sattler (2005).
Extending the size of protein-RNA complexes studied by nuclear magnetic resonance spectroscopy.
  Chembiochem, 6, 1578-1584.  
14730023 H.Banerjee, A.Rahn, B.Gawande, S.Guth, J.Valcarcel, and R.Singh (2004).
The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro.
  RNA, 10, 240-253.  
15200955 M.Blanchette, E.Labourier, R.E.Green, S.E.Brenner, and D.C.Rio (2004).
Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs.
  Mol Cell, 14, 775-786.  
12554879 H.Banerjee, A.Rahn, W.Davis, and R.Singh (2003).
Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF65) recognize polypyrimidine tracts using multiple modes of binding.
  RNA, 9, 88-99.  
12773396 J.M.Pérez Cañadillas, and G.Varani (2003).
Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein.
  EMBO J, 22, 2821-2830.
PDB code: 1p1t
14506271 O.A.Kent, A.Reayi, L.Foong, K.A.Chilibeck, and A.M.MacMillan (2003).
Structuring of the 3' splice site by U2AF65.
  J Biol Chem, 278, 50572-50577.  
12388766 P.Björk, G.Baurén, S.Jin, Y.G.Tong, T.R.Bürglin, U.Hellman, and L.Wieslander (2002).
A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis.
  Mol Biol Cell, 13, 3683-3695.  
12082087 P.S.Katsamba, M.Bayramyan, I.S.Haworth, D.G.Myszka, and I.A.Laird-Offringa (2002).
Complex role of the beta 2-beta 3 loop in the interaction of U1A with U1 hairpin II RNA.
  J Biol Chem, 277, 33267-33274.  
10856256 M.R.Conte, T.Grüne, J.Ghuman, G.Kelly, A.Ladas, S.Matthews, and S.Curry (2000).
Structure of tandem RNA recognition motifs from polypyrimidine tract binding protein reveals novel features of the RRM fold.
  EMBO J, 19, 3132-3141.
PDB code: 1qm9
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.