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PDBsum entry 1jmt

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protein ligands Protein-protein interface(s) links
RNA binding protein PDB id
1jmt
Jmol
Contents
Protein chains
98 a.a. *
23 a.a. *
Ligands
HEZ ×2
Waters ×118
* Residue conservation analysis
PDB id:
1jmt
Name: RNA binding protein
Title: X-ray structure of a core u2af65/u2af35 heterodimer
Structure: Splicing factor u2af 35 kda subunit. Chain: a. Synonym: u2 snrnp auxiliary factor small subunit. Engineered: yes. Mutation: yes. Splicing factor u2af 65 kda subunit. Chain: b. Synonym: u2 snrnp auxiliary factor large subunit. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Octamer (from PQS)
Resolution:
2.20Å     R-factor:   0.226     R-free:   0.238
Authors: C.L.Kielkopf,N.A.Rodionova,M.R.Green,S.K.Burley
Key ref:
C.L.Kielkopf et al. (2001). A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer. Cell, 106, 595-605. PubMed id: 11551507 DOI: 10.1016/S0092-8674(01)00480-9
Date:
19-Jul-01     Release date:   19-Sep-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q01081  (U2AF1_HUMAN) -  Splicing factor U2AF 35 kDa subunit
Seq:
Struc:
240 a.a.
98 a.a.*
Protein chain
Pfam   ArchSchema ?
P26368  (U2AF2_HUMAN) -  Splicing factor U2AF 65 kDa subunit
Seq:
Struc:
475 a.a.
23 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1016/S0092-8674(01)00480-9 Cell 106:595-605 (2001)
PubMed id: 11551507  
 
 
A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer.
C.L.Kielkopf, N.A.Rodionova, M.R.Green, S.K.Burley.
 
  ABSTRACT  
 
U2 auxiliary factor (U2AF) is an essential splicing factor that recognizes the 3' splice site and recruits the U2 snRNP to the branch point. The X-ray structure of the human core U2AF heterodimer, consisting of the U2AF35 central domain and a proline-rich region of U2AF65, has been determined at 2.2 A resolution. The structure reveals a novel protein-protein recognition strategy, in which an atypical RNA recognition motif (RRM) of U2AF35 and the U2AF65 polyproline segment interact via reciprocal "tongue-in-groove" tryptophan residues. Complementary biochemical experiments demonstrate that the core U2AF heterodimer binds RNA, and that the interacting tryptophan side chains are essential for U2AF dimerization. Atypical RRMs in other splicing factors may serve as protein-protein interaction motifs elsewhere during spliceosome assembly.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of the U2AF^35/U2AF^65 Complex(A) Stereoview of the U2AF^65 proline-rich loop enveloping U2AF^35 Trp134. Density modified, experimental electron density map for residues Trp92p to Pro104p of U2AF^65 contoured at 1σ. The U2AF^65 peptide is shown in pink, or color coded for atom type (yellow, carbon; red, oxygen; and blue, nitrogen) and the U2AF^35 domain is shown in light blue. Six disordered amino acids linking α helix A with the RNP2 β strand 1 are represented with a dashed line. The RNP motifs and α helices A and B are labeled.(B) The U2AF complex viewed along the cylindrical axis of α helix A. A schematic representation of the reciprocal tryptophan binding sites is shown on the left.(C) View of the binary complex perpendicular to the perspective of (B).(D) U2AF^35 β sheet that forms the RNA binding surfaces of canonical RRM-containing proteins
Figure 3.
Figure 3. Reciprocal Tryptophan Recognition within the U2AF HeterodimerStereodrawings of interactions with (A) U2AF^35 Trp134 and (B) U2AF^65 Trp92p
 
  The above figures are reprinted by permission from Cell Press: Cell (2001, 106, 595-605) copyright 2001.  
  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
22158538 T.A.Graubert, D.Shen, L.Ding, T.Okeyo-Owuor, C.L.Lunn, J.Shao, K.Krysiak, C.C.Harris, D.C.Koboldt, D.E.Larson, M.D.McLellan, D.J.Dooling, R.M.Abbott, R.S.Fulton, H.Schmidt, J.Kalicki-Veizer, M.O'Laughlin, M.Grillot, J.Baty, S.Heath, J.L.Frater, T.Nasim, D.C.Link, M.H.Tomasson, P.Westervelt, J.F.DiPersio, E.R.Mardis, T.J.Ley, R.K.Wilson, and M.J.Walter (2012).
Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes.
  Nat Genet, 44, 53-57.  
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
21166792 R.B.McCole, N.B.Loughran, M.Chahal, L.P.Fernandes, R.G.Roberts, F.Fraternali, M.J.O'Connell, and R.J.Oakey (2011).
A case-by-case evolutionary analysis of four imprinted retrogenes.
  Evolution, 65, 1413-1427.  
21253573 R.B.Tunnicliffe, G.M.Hautbergue, P.Kalra, B.R.Jackson, A.Whitehouse, S.A.Wilson, and A.P.Golovanov (2011).
Structural basis for the recognition of cellular mRNA export factor REF by herpes viral proteins HSV-1 ICP27 and HVS ORF57.
  PLoS Pathog, 7, e1001244.
PDB code: 2kt5
21292163 Y.Bai, S.K.Srivastava, J.H.Chang, J.L.Manley, and L.Tong (2011).
Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase.
  Mol Cell, 41, 311-320.
PDB code: 3pq1
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.  
20628762 J.Kralovicova, and I.Vorechovsky (2010).
Allele-specific recognition of the 3' splice site of INS intron 1.
  Hum Genet, 128, 383-400.  
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
19540372 J.R.Prigge, S.V.Iverson, A.M.Siders, and E.E.Schmidt (2009).
Interactome for auxiliary splicing factor U2AF(65) suggests diverse roles.
  Biochim Biophys Acta, 1789, 487-492.  
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.  
18460468 F.Heyd, M.Carmo-Fonseca, and T.Möröy (2008).
Differential isoform expression and interaction with the P32 regulatory protein controls the subcellular localization of the splicing factor U2AF26.
  J Biol Chem, 283, 19636-19645.  
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.  
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.  
18211889 J.T.Little, and M.S.Jurica (2008).
Splicing factor SPF30 bridges an interaction between the prespliceosome protein U2AF35 and tri-small nuclear ribonucleoprotein protein hPrp3.
  J Biol Chem, 283, 8145-8152.  
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
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
17785461 P.Nilsson, N.Henriksson, A.Niedzwiecka, N.A.Balatsos, K.Kokkoris, J.Eriksson, and A.Virtanen (2007).
A multifunctional RNA recognition motif in poly(A)-specific ribonuclease with cap and poly(A) binding properties.
  J Biol Chem, 282, 32902-32911.  
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.  
16407336 C.Haynes, and L.M.Iakoucheva (2006).
Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins.
  Nucleic Acids Res, 34, 305-312.  
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.  
17042780 I.Mollet, N.L.Barbosa-Morais, J.Andrade, and M.Carmo-Fonseca (2006).
Diversity of human U2AF splicing factors.
  FEBS J, 273, 4807-4816.  
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.  
16809543 L.M.Soares, K.Zanier, C.Mackereth, M.Sattler, and J.Valcárcel (2006).
Intron removal requires proofreading of U2AF/3' splice site recognition by DEK.
  Science, 312, 1961-1965.  
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
17024186 S.Millevoi, C.Loulergue, S.Dettwiler, S.Z.Karaa, W.Keller, M.Antoniou, and S.Vagner (2006).
An interaction between U2AF 65 and CF I(m) links the splicing and 3' end processing machineries.
  EMBO J, 25, 4854-4864.  
16940179 T.R.Pacheco, M.B.Coelho, J.M.Desterro, I.Mollet, and M.Carmo-Fonseca (2006).
In vivo requirement of the small subunit of U2AF for recognition of a weak 3' splice site.
  Mol Cell Biol, 26, 8183-8190.  
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.  
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.  
16116489 E.Meshorer, B.Bryk, D.Toiber, J.Cohen, E.Podoly, A.Dori, and H.Soreq (2005).
SC35 promotes sustainable stress-induced alternative splicing of neuronal acetylcholinesterase mRNA.
  Mol Psychiatry, 10, 985-997.  
16043505 J.Chusainow, P.M.Ajuh, L.Trinkle-Mulcahy, J.E.Sleeman, J.Ellenberg, and A.I.Lamond (2005).
FRET analyses of the U2AF complex localize the U2AF35/U2AF65 interaction in vivo and reveal a novel self-interaction of U2AF35.
  RNA, 11, 1201-1214.  
16077728 R.Singh, and J.Valcárcel (2005).
Building specificity with nonspecific RNA-binding proteins.
  Nat Struct Mol Biol, 12, 645-653.  
16227607 T.N.Siegel, K.S.Tan, and G.A.Cross (2005).
Systematic study of sequence motifs for RNA trans splicing in Trypanosoma brucei.
  Mol Cell Biol, 25, 9586-9594.  
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.  
15342650 L.Jeffery, and S.Nakielny (2004).
Components of the DNA methylation system of chromatin control are RNA-binding proteins.
  J Biol Chem, 279, 49479-49487.  
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.  
14981503 M.S.Jurica, D.Sousa, M.J.Moore, and N.Grigorieff (2004).
Three-dimensional structure of C complex spliceosomes by electron microscopy.
  Nat Struct Mol Biol, 11, 265-269.  
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.  
15096518 T.R.Pacheco, A.Q.Gomes, N.L.Barbosa-Morais, V.Benes, W.Ansorge, M.Wollerton, C.W.Smith, J.Valcárcel, and M.Carmo-Fonseca (2004).
Diversity of vertebrate splicing factor U2AF35: identification of alternatively spliced U2AF1 mRNAS.
  J Biol Chem, 279, 27039-27049.  
12737811 G.Varani, and A.Ramos (2003).
Splicing factor 1 in the pocket.
  Structure, 11, 481-482.  
14576315 H.Gu, and D.R.Schoenberg (2003).
U2AF modulates poly(A) length control by the poly(A)-limiting element.
  Nucleic Acids Res, 31, 6264-6271.  
12704080 H.Shi, and R.M.Xu (2003).
Crystal structure of the Drosophila Mago nashi-Y14 complex.
  Genes Dev, 17, 971-976.
PDB code: 1oo0
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.  
12730685 S.Fribourg, D.Gatfield, E.Izaurralde, and E.Conti (2003).
A novel mode of RBD-protein recognition in the Y14-Mago complex.
  Nat Struct Biol, 10, 433-439.
PDB code: 1hl6
11739736 J.Shepard, M.Reick, S.Olson, and B.R.Graveley (2002).
Characterization of U2AF(6), a splicing factor related to U2AF(35).
  Mol Cell Biol, 22, 221-230.  
12419246 J.W.Wu, A.R.Krawitz, J.Chai, W.Li, F.Zhang, K.Luo, and Y.Shi (2002).
Structural mechanism of Smad4 recognition by the nuclear oncoprotein Ski: insights on Ski-mediated repression of TGF-beta signaling.
  Cell, 111, 357-367.
PDB code: 1mr1
12486009 P.Förch, O.Puig, C.Martínez, B.Séraphin, and J.Valcárcel (2002).
The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5' splice sites.
  EMBO J, 21, 6882-6892.  
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.