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PDBsum entry 1o0p

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protein Protein-protein interface(s) links
RNA binding protein PDB id
1o0p
Jmol
Contents
Protein chains
104 a.a. *
13 a.a. *
* Residue conservation analysis
PDB id:
1o0p
Name: RNA binding protein
Title: Solution structure of the third RNA recognition motif (rrm) of u2af65 in complex with an n-terminal sf1 peptide
Structure: Splicing factor u2af 65 kda subunit. Chain: a. Fragment: c-terminal rrm domain. Synonym: u2 auxiliary factor 65 kda subunit, u2 snrnp auxiliary factor large subunit, hu2af(65). Engineered: yes. Splicing factor sf1. Chain: b. Fragment: n-terminal peptide.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the peptide was chemically synthesized and derived from the n-terminus of sf1. The sequence of the peptide is naturally found in homo sapiens (human).
NMR struc: 10 models
Authors: P.Selenko,G.Gregorovic,R.Sprangers,G.Stier,Z.Rhani,A.Kramer, M.Sattler
Key ref:
P.Selenko et al. (2003). Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. Mol Cell, 11, 965-976. PubMed id: 12718882 DOI: 10.1016/S1097-2765(03)00115-1
Date:
24-Feb-03     Release date:   06-May-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26368  (U2AF2_HUMAN) -  Splicing factor U2AF 65 kDa subunit
Seq:
Struc:
475 a.a.
104 a.a.
Protein chain
Pfam   ArchSchema ?
Q15637  (SF01_HUMAN) -  Splicing factor 1
Seq:
Struc:
 
Seq:
Struc:
639 a.a.
13 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1016/S1097-2765(03)00115-1 Mol Cell 11:965-976 (2003)
PubMed id: 12718882  
 
 
Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP.
P.Selenko, G.Gregorovic, R.Sprangers, G.Stier, Z.Rhani, A.Krämer, M.Sattler.
 
  ABSTRACT  
 
The essential splicing factors SF1 and U2AF play an important role in the recognition of the pre-mRNA 3' splice site during early spliceosome assembly. The structure of the C-terminal RRM (RRM3) of human U2AF(65) complexed to an N-terminal peptide of SF1 reveals an extended negatively charged helix A and an additional helix C. Helix C shields the potential RNA binding surface. SF1 binds to the opposite, helical face of RRM3. It inserts a conserved tryptophan into a hydrophobic pocket between helices A and B in a way that strikingly resembles part of the molecular interface in the U2AF heterodimer. This molecular recognition establishes a paradigm for protein binding by a subfamily of noncanonical RRMs.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Tryptophan Recognition by the U2AF^35 RRM and U2AF^65-RRM3(A) Ribbon representation of the U2AF^35 RRM in complex with the proline-rich region in the N terminus of U2AF^65 (Kielkopf et al., 2001). Side chains involved in the molecular interface are shown. Trp134, which is not conserved in U2AF^65-RRM3, is labeled magenta.(B) Ribbon representation of the U2AF^65-RRM3/SF1 complex. Side chains involved in tryptophan coordination are shown.(C) Sequence alignment of noncanonical RRMs with an extended and negatively charged helix A. Conserved residues that mediate recognition of SF1 Trp22 and U2AF^65 Trp92 by U2AF^65-RRM3 and the U2AF^35 RRM, respectively, are shown in white on black. Trp134 in the U2AF^35 RRM is colored magenta.(D) Domain organization of proteins that contain noncanonical RRMs. The domain annotations are according to SMART (Schultz et al., 1998). “R/S” is an arginine-serine-rich region, “STY Kc” is a phoshokinase domain, and “Zn” are zinc binding domains.
Figure 6.
Figure 6. Structure and Topology of Complex E during Spliceosome AssemblyFor a description, see the text. An additional interaction between the R/S domain of U2AF^65 and the BPS (Valcárcel et al., 1996) is not shown.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 11, 965-976) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22388736 A.G.Murachelli, J.Ebert, C.Basquin, H.Le Hir, and E.Conti (2012).
The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex.
  Nat Struct Mol Biol, 19, 378-386.
PDB codes: 4a6q 4a8x 4a90
21062807 M.Corioni, N.Antih, G.Tanackovic, M.Zavolan, and A.Krämer (2011).
Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing.
  Nucleic Acids Res, 39, 1868-1879.  
21295486 Q.Yang, M.Coseno, G.M.Gilmartin, and S.Doublié (2011).
Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping.
  Structure, 19, 368-377.
PDB codes: 3q2s 3q2t
20711187 C.D.Cukier, D.Hollingworth, S.R.Martin, G.Kelly, I.Díaz-Moreno, and A.Ramos (2010).
Molecular basis of FIR-mediated c-myc transcriptional control.
  Nat Struct Mol Biol, 17, 1058-1064.  
20360394 J.Chang, B.Schwer, and S.Shuman (2010).
Mutational analyses of trimethylguanosine synthase (Tgs1) and Mud2: proteins implicated in pre-mRNA splicing.
  RNA, 16, 1018-1031.  
20060839 L.Elantak, S.Wagner, A.Herrmannová, M.Karásková, E.Rutkai, P.J.Lukavsky, and L.Valásek (2010).
The indispensable N-terminal half of eIF3j/HCR1 cooperates with its structurally conserved binding partner eIF3b/PRT1-RRM and with eIF1A in stringent AUG selection.
  J Mol Biol, 396, 1097-1116.  
19295135 A.Eulalio, F.Tritschler, R.Büttner, O.Weichenrieder, E.Izaurralde, and V.Truffault (2009).
The RRM domain in GW182 proteins contributes to miRNA-mediated gene silencing.
  Nucleic Acids Res, 37, 2974-2983.
PDB code: 2wbr
20037628 C.de Chiara, R.P.Menon, M.Strom, T.J.Gibson, and A.Pastore (2009).
Phosphorylation of s776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors.
  PLoS One, 4, e8372.  
19523901 J.H.Lee, E.S.Rangarajan, S.D.Yogesha, and T.Izard (2009).
Raver1 interactions with vinculin and RNA suggest a feed-forward pathway in directing mRNA to focal adhesions.
  Structure, 17, 833-842.
PDB codes: 3h2u 3h2v
18974054 L.Corsini, M.Hothorn, G.Stier, V.Rybin, K.Scheffzek, T.J.Gibson, and M.Sattler (2009).
Dimerization and Protein Binding Specificity of the U2AF Homology Motif of the Splicing Factor Puf60.
  J Biol Chem, 284, 630-639.
PDB code: 3dxb
19893607 L.Ma, and H.R.Horvitz (2009).
Mutations in the Caenorhabditis elegans U2AF large subunit UAF-1 alter the choice of a 3' splice site in vivo.
  PLoS Genet, 5, e1000708.  
19033360 M.A.Brooks, A.Dziembowski, S.Quevillon-Cheruel, V.Henriot, C.Faux, H.van Tilbeurgh, and B.Séraphin (2009).
Structure of the yeast Pml1 splicing factor and its integration into the RES complex.
  Nucleic Acids Res, 37, 129-143.
PDB code: 2jkd
18515081 A.Cléry, M.Blatter, and F.H.Allain (2008).
RNA recognition motifs: boring? Not quite.
  Curr Opin Struct Biol, 18, 290-298.  
18158581 C.R.Mandel, Y.Bai, and L.Tong (2008).
Protein factors in pre-mRNA 3'-end processing.
  Cell Mol Life Sci, 65, 1099-1122.  
18203745 G.Toba, and K.White (2008).
The third RNA recognition motif of Drosophila ELAV protein has a role in multimerization.
  Nucleic Acids Res, 36, 1390-1399.  
18559344 I.Keren, L.Klipcan, A.Bezawork-Geleta, M.Kolton, F.Shaya, and O.Ostersetzer-Biran (2008).
Characterization of the Molecular Basis of Group II Intron RNA Recognition by CRS1-CRM Domains.
  J Biol Chem, 283, 23333-23342.  
18842594 J.L.Jenkins, H.Shen, M.R.Green, and C.L.Kielkopf (2008).
Solution Conformation and Thermodynamic Characteristics of RNA Binding by the Splicing Factor U2AF65.
  J Biol Chem, 283, 33641-33649.  
18508922 J.M.Izquierdo (2008).
Fas splicing regulation during early apoptosis is linked to caspase-mediated cleavage of U2AF65.
  Mol Biol Cell, 19, 3299-3307.  
18285458 J.Rino, J.M.Desterro, T.R.Pacheco, T.W.Gadella, and M.Carmo-Fonseca (2008).
Splicing factors SF1 and U2AF associate in extraspliceosomal complexes.
  Mol Cell Biol, 28, 3045-3057.  
19000813 J.Sperling, M.Azubel, and R.Sperling (2008).
Structure and function of the Pre-mRNA splicing machine.
  Structure, 16, 1605-1615.  
18076038 K.Kuwasako, N.Dohmae, M.Inoue, M.Shirouzu, S.Taguchi, P.Güntert, B.Séraphin, Y.Muto, and S.Yokoyama (2008).
Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses.
  Proteins, 71, 1617-1636.  
19043415 M.Teplova, and D.J.Patel (2008).
Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1.
  Nat Struct Mol Biol, 15, 1343-1351.
PDB codes: 3d2n 3d2q 3d2s
18054235 P.Tompa, and M.Fuxreiter (2008).
Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions.
  Trends Biochem Sci, 33, 2-8.  
18809678 S.Trowitzsch, G.Weber, R.Lührmann, and M.C.Wahl (2008).
An unusual RNA recognition motif acts as a scaffold for multiple proteins in the pre-mRNA retention and splicing complex.
  J Biol Chem, 283, 32317-32327.  
18588901 V.Manceau, C.L.Kielkopf, A.Sobel, and A.Maucuer (2008).
Different requirements of the kinase and UHM domains of KIS for its nuclear localization and binding to splicing factors.
  J Mol Biol, 381, 748-762.  
17473849 B.M.Lunde, C.Moore, and G.Varani (2007).
RNA-binding proteins: modular design for efficient function.
  Nat Rev Mol Cell Biol, 8, 479-490.  
17229474 D.M.Lehmann, C.A.Galloway, C.MacElrevey, M.P.Sowden, J.E.Wedekind, and H.C.Smith (2007).
Functional characterization of APOBEC-1 complementation factor phosphorylation sites.
  Biochim Biophys Acta, 1773, 408-418.  
17589525 L.Corsini, S.Bonnal, S.Bonna, J.Basquin, M.Hothorn, K.Scheffzek, J.Valcárcel, and M.Sattler (2007).
U2AF-homology motif interactions are required for alternative splicing regulation by SPF45.
  Nat Struct Mol Biol, 14, 620-629.
PDB codes: 2pe8 2peh
17190833 L.ElAntak, A.G.Tzakos, N.Locker, and P.J.Lukavsky (2007).
Structure of eIF3b RNA recognition motif and its interaction with eIF3j: structural insights into the recruitment of eIF3b to the 40 S ribosomal subunit.
  J Biol Chem, 282, 8165-8174.
PDB code: 2nlw
17786225 S.D.Shaw, S.Chakrabarti, G.Ghosh, and A.R.Krainer (2007).
Deletion of the N-terminus of SF2/ASF permits RS-domain-independent pre-mRNA splicing.
  PLoS ONE, 2, e854.  
16936729 A.P.Rideau, C.Gooding, P.J.Simpson, T.P.Monie, M.Lorenz, S.Hüttelmaier, R.H.Singer, S.Matthews, S.Curry, and C.W.Smith (2006).
A peptide motif in Raver1 mediates splicing repression by interaction with the PTB RRM2 domain.
  Nat Struct Mol Biol, 13, 839-848.  
16431982 I.A.Turner, C.M.Norman, M.J.Churcher, and A.J.Newman (2006).
Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome.
  RNA, 12, 375-386.  
16376933 K.R.Thickman, M.C.Swenson, J.M.Kabogo, Z.Gryczynski, and C.L.Kielkopf (2006).
Multiple U2AF65 binding sites within SF3b155: thermodynamic and spectroscopic characterization of protein-protein interactions among pre-mRNA splicing factors.
  J Mol Biol, 356, 664-683.  
16432215 M.J.Schellenberg, R.A.Edwards, D.B.Ritchie, O.A.Kent, M.M.Golas, H.Stark, R.Lührmann, J.N.Glover, and A.M.MacMillan (2006).
Crystal structure of a core spliceosomal protein interface.
  Proc Natl Acad Sci U S A, 103, 1266-1271.
PDB codes: 2f9d 2f9j
16495236 R.Spadaccini, U.Reidt, O.Dybkov, C.Will, R.Frank, G.Stier, L.Corsini, M.C.Wahl, R.Lührmann, and M.Sattler (2006).
Biochemical and NMR analyses of an SF3b155-p14-U2AF-RNA interaction network involved in branch point definition during pre-mRNA splicing.
  RNA, 12, 410-425.  
16648637 S.Caputo, J.Couprie, I.Duband-Goulet, E.Kondé, F.Lin, S.Braud, M.Gondry, B.Gilquin, H.J.Worman, and S.Zinn-Justin (2006).
The carboxyl-terminal nucleoplasmic region of MAN1 exhibits a DNA binding winged helix domain.
  J Biol Chem, 281, 18208-18215.
PDB code: 2ch0
16420481 V.Manceau, M.Swenson, J.P.Le Caer, A.Sobel, C.L.Kielkopf, and A.Maucuer (2006).
Major phosphorylation of SF1 on adjacent Ser-Pro motifs enhances interaction with U2AF65.
  FEBS J, 273, 577-587.  
16148043 A.H.Fox, C.S.Bond, and A.I.Lamond (2005).
P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner.
  Mol Biol Cell, 16, 5304-5315.  
15701634 A.Savchenko, N.Krogan, J.R.Cort, E.Evdokimova, J.M.Lew, A.A.Yee, L.Sánchez-Pulido, M.A.Andrade, A.Bochkarev, J.D.Watson, M.A.Kennedy, J.Greenblatt, T.Hughes, C.H.Arrowsmith, J.M.Rommens, and A.M.Edwards (2005).
The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.
  J Biol Chem, 280, 19213-19220.
PDB codes: 1nyn 1p9q
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.  
15548596 C.J.Webb, S.Lakhe-Reddy, C.M.Romfo, and J.A.Wise (2005).
Analysis of mutant phenotypes and splicing defects demonstrates functional collaboration between the large and small subunits of the essential splicing factor U2AF in vivo.
  Mol Biol Cell, 16, 584-596.  
15853797 C.Maris, C.Dominguez, and F.H.Allain (2005).
The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression.
  FEBS J, 272, 2118-2131.  
15647371 G.Tanackovic, and A.Krämer (2005).
Human splicing factor SF3a, but not SF1, is essential for pre-mRNA splicing in vivo.
  Mol Biol Cell, 16, 1366-1377.  
16077728 R.Singh, and J.Valcárcel (2005).
Building specificity with nonspecific RNA-binding proteins.
  Nat Struct Mol Biol, 12, 645-653.  
16109373 S.Sharma, A.M.Falick, and D.L.Black (2005).
Polypyrimidine tract binding protein blocks the 5' splice site-dependent assembly of U2AF and the prespliceosomal E complex.
  Mol Cell, 19, 485-496.  
15853794 Y.Chen, and G.Varani (2005).
Protein families and RNA recognition.
  FEBS J, 272, 2088-2097.  
15121844 C.J.Webb, and J.A.Wise (2004).
The splicing factor U2AF small subunit is functionally conserved between fission yeast and humans.
  Mol Cell Biol, 24, 4229-4240.  
15231733 C.L.Kielkopf, S.Lücke, and M.R.Green (2004).
U2AF homology motifs: protein recognition in the RRM world.
  Genes Dev, 18, 1513-1526.  
15165181 E.Gendra, A.Moreno, M.M.Albà, and M.Pages (2004).
Interaction of the plant glycine-rich RNA-binding protein MA16 with a novel nucleolar DEAD box RNA helicase protein from Zea mays.
  Plant J, 38, 875-886.  
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.  
15004547 J.Kadlec, E.Izaurralde, and S.Cusack (2004).
The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3.
  Nat Struct Mol Biol, 11, 330-337.
PDB code: 1uw4
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.  
15169763 S.Dettwiler, C.Aringhieri, S.Cardinale, W.Keller, and S.M.Barabino (2004).
Distinct sequence motifs within the 68-kDa subunit of cleavage factor Im mediate RNA binding, protein-protein interactions, and subcellular localization.
  J Biol Chem, 279, 35788-35797.  
12737811 G.Varani, and A.Ramos (2003).
Splicing factor 1 in the pocket.
  Structure, 11, 481-482.  
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.  
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.