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PDBsum entry 1b7f

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protein dna_rna Protein-protein interface(s) links
RNA-binding protein/RNA PDB id
1b7f
Jmol
Contents
Protein chains
167 a.a. *
DNA/RNA
Waters ×84
* Residue conservation analysis
PDB id:
1b7f
Name: RNA-binding protein/RNA
Title: Sxl-lethal protein/RNA complex
Structure: RNA (5'-r(p Gp Up Up Gp Up Up Up Up Up Up Up U)-3 chain: p, q. Synonym: tra pre-mRNA. Engineered: yes. Protein (sxl-lethal protein). Chain: a, b. Fragment: 2 rnp-domains. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Other_details: origin of the sequence: drosophila melanogas nucleus. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Cellular_location: nucleus. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.201     R-free:   0.294
Authors: N.Handa,O.Nureki,K.Kurimoto,I.Kim,H.Sakamoto,Y.Shimura,Y.Mut S.Yokoyama,Riken Structural Genomics/proteomics Initiative
Key ref:
N.Handa et al. (1999). Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature, 398, 579-585. PubMed id: 10217141 DOI: 10.1038/19242
Date:
23-Jan-99     Release date:   03-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19339  (SXL_DROME) -  Protein sex-lethal
Seq:
Struc:
354 a.a.
167 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!
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1038/19242 Nature 398:579-585 (1999)
PubMed id: 10217141  
 
 
Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein.
N.Handa, O.Nureki, K.Kurimoto, I.Kim, H.Sakamoto, Y.Shimura, Y.Muto, S.Yokoyama.
 
  ABSTRACT  
 
The Sex-lethal (Sxl) protein of Drosophila melanogaster regulates alternative splicing of the transformer (tra) messenger RNA precursor by binding to the tra polypyrimidine tract during the sex-determination process. The crystal structure has now been determined at 2.6 A resolution of the complex formed between two tandemly arranged RNA-binding domains of the Sxl protein and a 12-nucleotide, single-stranded RNA derived from the tra polypyrimidine tract. The two RNA-binding domains have their beta-sheet platforms facing each other to form a V-shaped cleft. The RNA is characteristically extended and bound in this cleft, where the UGUUUUUUU sequence is specifically recognized by the protein. This structure offers the first insight, to our knowledge, into how a protein binds specifically to a cognate RNA without any intramolecular base-pairing.
 
  Selected figure(s)  
 
Figure 3.
Figure 3: Distribution of the electrostatic potential on the solvent-accessible surface of Sxl (stereo view). The bound 12-nucleotide RNA is indicated in yellow by a ball-and-stick representation. The V-shaped interdomain cleft and the surface on the RBD2 -sheet platform are strongly electropositive (blue); these accommodate the phosphodiester backbone of the elongated RNA well. On the other hand, electronegative regions (red) are scattered. This figure was drawn using MOLMOL^50.
Figure 4.
Figure 4: The U3–U11 (UGUUUUUUU) RNA segment in the complex (stereo view). RNA is represented by a wire-loop model in yellow, with atoms of nitrogen, oxygen and phosphorus shown in blue, red and purple, respectively. The ribose moieties, except for U8, are in the C2'-endo form. Light green broken lines show the intramolecular hydrogen bonds that characterize the turn conformation of RNA. The side chains of the amino acids that interact with the RNA backbone are represented in green. Red broken lines denote the intermolecular hydrogen bonds of the amino-acid side chains with the phosphate–sugar backbone.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 398, 579-585) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20805243 B.M.Lunde, M.Hörner, and A.Meinhart (2011).
Structural insights into cis element recognition of non-polyadenylated RNAs by the Nab3-RRM.
  Nucleic Acids Res, 39, 337-346.
PDB codes: 2xnq 2xnr
21419778 D.Anunciado, A.Dhar, M.Gruebele, and A.M.Baranger (2011).
Multistep kinetics of the U1A-SL2 RNA complex dissociation.
  J Mol Biol, 408, 896-908.  
21572444 E.M.Gesner, M.J.Schellenberg, E.L.Garside, M.M.George, and A.M.Macmillan (2011).
Recognition and maturation of effector RNAs in a CRISPR interference pathway.
  Nat Struct Mol Biol, 18, 688-692.
PDB codes: 3qrp 3qrq 3qrr
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
19846595 F.Bolognani, T.Contente-Cuomo, and N.I.Perrone-Bizzozero (2010).
Novel recognition motifs and biological functions of the RNA-binding protein HuD revealed by genome-wide identification of its targets.
  Nucleic Acids Res, 38, 117-130.  
20479262 Q.Yang, G.M.Gilmartin, and S.Doublié (2010).
Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing.
  Proc Natl Acad Sci U S A, 107, 10062-10067.
PDB codes: 3mdg 3mdi
  20862284 S.Khoshnevis, P.Neumann, and R.Ficner (2010).
Crystal structure of the RNA recognition motif of yeast translation initiation factor eIF3b reveals differences to human eIF3b.
  PLoS One, 5, 0.
PDB codes: 3ns5 3ns6
19553194 K.Tsuda, K.Kuwasako, M.Takahashi, T.Someya, M.Inoue, T.Terada, N.Kobayashi, M.Shirouzu, T.Kigawa, A.Tanaka, S.Sugano, P.Güntert, Y.Muto, and S.Yokoyama (2009).
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3.
  Nucleic Acids Res, 37, 5151-5166.
PDB codes: 2rq4 2rqc
19865697 L.L.Cline, and M.L.Waters (2009).
Design of a beta-hairpin peptide-intercalator conjugate for simultaneous recognition of single stranded and double stranded regions of RNA.
  Org Biomol Chem, 7, 4622-4630.  
18515081 A.Cléry, M.Blatter, and F.H.Allain (2008).
RNA recognition motifs: boring? Not quite.
  Curr Opin Struct Biol, 18, 290-298.  
18201561 A.O.Kumar, M.C.Swenson, M.M.Benning, and C.L.Kielkopf (2008).
Structure of the central RNA recognition motif of human TIA-1 at 1.95A resolution.
  Biochem Biophys Res Commun, 367, 813-819.
PDB code: 3bs9
18255277 A.Serganov, and D.J.Patel (2008).
Towards deciphering the principles underlying an mRNA recognition code.
  Curr Opin Struct Biol, 18, 120-129.  
18452949 A.Shulman-Peleg, M.Shatsky, R.Nussinov, and H.J.Wolfson (2008).
Prediction of interacting single-stranded RNA bases by protein-binding patterns.
  J Mol Biol, 379, 299-316.  
18293956 D.Anunciado, M.Agumeh, B.L.Kormos, D.L.Beveridge, J.L.Knee, and A.M.Baranger (2008).
Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements.
  J Phys Chem B, 112, 6122-6130.  
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.  
18059478 G.V.Crichlow, H.Zhou, H.H.Hsiao, K.B.Frederick, M.Debrosse, Y.Yang, E.J.Folta-Stogniew, H.J.Chung, C.Fan, E.M.De la Cruz, D.Levens, E.Lolis, and D.Braddock (2008).
Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition.
  EMBO J, 27, 277-289.
PDB code: 2qfj
18275081 H.Ge, D.Zhou, S.Tong, Y.Gao, M.Teng, and L.Niu (2008).
Crystal structure and possible dimerization of the single RRM of human PABPN1.
  Proteins, 71, 1539-1545.
PDB codes: 3b4d 3b4m
18702462 J.Qian, D.Cuerrier, P.L.Davies, Z.Li, J.C.Powers, and R.L.Campbell (2008).
Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions.
  J Med Chem, 51, 5264-5270.
PDB codes: 2r9c 2r9f
18824697 J.Song, J.V.McGivern, K.W.Nichols, J.L.Markley, and M.D.Sheets (2008).
Structural basis for RNA recognition by a type II poly(A)-binding protein.
  Proc Natl Acad Sci U S A, 105, 15317-15322.
PDB code: 2jwn
19079550 K.N.Rao, S.K.Burley, and S.Swaminathan (2008).
UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function.
  PLoS ONE, 3, e3903.
PDB codes: 2nrq 2nwu 2ogk 2pzz
17967886 M.G.Suzuki, S.Imanishi, N.Dohmae, T.Nishimura, T.Shimada, and S.Matsumoto (2008).
Establishment of a novel in vivo sex-specific splicing assay system to identify a trans-acting factor that negatively regulates splicing of Bombyx mori dsx female exons.
  Mol Cell Biol, 28, 333-343.  
18022637 P.Deka, M.E.Bucheli, C.Moore, S.Buratowski, and G.Varani (2008).
Structure of the yeast SR protein Npl3 and Interaction with mRNA 3'-end processing signals.
  J Mol Biol, 375, 136-150.
PDB codes: 2osq 2osr
18186485 R.Worch, and R.Stolarski (2008).
Stacking efficiency and flexibility analysis of aromatic amino acids in cap-binding proteins.
  Proteins, 71, 2026-2037.  
18641416 T.Nagata, S.Suzuki, R.Endo, M.Shirouzu, T.Terada, M.Inoue, T.Kigawa, N.Kobayashi, P.Güntert, A.Tanaka, Y.Hayashizaki, Y.Muto, and S.Yokoyama (2008).
The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
  Nucleic Acids Res, 36, 4754-4767.
PDB code: 2rok
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.  
17508423 F.A.Rahman, J.F.Ainscough, N.Copeland, and D.Coverley (2007).
Cancer-associated missplicing of exon 4 influences the subnuclear distribution of the DNA replication factor CIZ1.
  Hum Mutat, 28, 993.  
18155131 M.Kedde, M.J.Strasser, B.Boldajipour, J.A.Oude Vrielink, K.Slanchev, C.le Sage, R.Nagel, P.M.Voorhoeve, J.van Duijse, U.A.Ørom, A.H.Lund, A.Perrakis, E.Raz, and R.Agami (2007).
RNA-binding protein Dnd1 inhibits microRNA access to target mRNA.
  Cell, 131, 1273-1286.  
16672237 A.Ebihara, M.Yao, R.Masui, I.Tanaka, S.Yokoyama, and S.Kuramitsu (2006).
Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain.
  Protein Sci, 15, 1494-1499.
PDB code: 1wj9
  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
16362043 F.Vitali, A.Henning, F.C.Oberstrass, Y.Hargous, S.D.Auweter, M.Erat, and F.H.Allain (2006).
Structure of the two most C-terminal RNA recognition motifs of PTB using segmental isotope labeling.
  EMBO J, 25, 150-162.
PDB code: 2evz
16493477 J.Barman, S.Acharya, C.Zhou, S.Chatterjee, A.Engström, and J.Chattopadhyaya (2006).
Non-identical electronic characters of the internucleotidic phosphates in RNA modulate the chemical reactivity of the phosphodiester bonds.
  Org Biomol Chem, 4, 928-941.  
16794580 J.M.Pérez-Cañadillas (2006).
Grabbing the message: structural basis of mRNA 3'UTR recognition by Hrp1.
  EMBO J, 25, 3167-3178.
PDB code: 2cjk
16923806 J.Mercante, K.Suzuki, X.Cheng, P.Babitzke, and T.Romeo (2006).
Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance.
  J Biol Chem, 281, 31832-31842.  
16407334 M.J.Law, M.E.Linde, E.J.Chambers, C.Oubridge, P.S.Katsamba, L.Nilsson, I.S.Haworth, and I.A.Laird-Offringa (2006).
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA.
  Nucleic Acids Res, 34, 275-285.  
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
16387655 M.Teplova, Y.R.Yuan, A.T.Phan, L.Malinina, S.Ilin, A.Teplov, and D.J.Patel (2006).
Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen.
  Mol Cell, 21, 75-85.
PDB codes: 1yty 1zh5
16462747 S.A.Jacobs, E.R.Podell, and T.R.Cech (2006).
Crystal structure of the essential N-terminal domain of telomerase reverse transcriptase.
  Nat Struct Mol Biol, 13, 218-225.
PDB code: 2b2a
16982642 S.D.Auweter, F.C.Oberstrass, and F.H.Allain (2006).
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
  Nucleic Acids Res, 34, 4943-4959.  
16362037 S.D.Auweter, R.Fasan, L.Reymond, J.G.Underwood, D.L.Black, S.Pitsch, and F.H.Allain (2006).
Molecular basis of RNA recognition by the human alternative splicing factor Fox-1.
  EMBO J, 25, 163-173.
PDB code: 2err
16611943 S.Wang, Y.Hu, M.T.Overgaard, F.V.Karginov, O.C.Uhlenbeck, and D.B.McKay (2006).
The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold.
  RNA, 12, 959-967.
PDB code: 2g0c
17036044 Y.Hargous, G.M.Hautbergue, A.M.Tintaru, L.Skrisovska, A.P.Golovanov, J.Stevenin, L.Y.Lian, S.A.Wilson, and F.H.Allain (2006).
Molecular basis of RNA recognition and TAP binding by the SR proteins SRp20 and 9G8.
  EMBO J, 25, 5126-5137.
PDB codes: 2hvz 2i2y 2i38
16278830 Y.Zhao, B.L.Kormos, D.L.Beveridge, and A.M.Baranger (2006).
Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface.
  Biopolymers, 81, 256-269.  
16193062 B.Beuth, S.Pennell, K.B.Arnvig, S.R.Martin, and I.A.Taylor (2005).
Structure of a Mycobacterium tuberculosis NusA-RNA complex.
  EMBO J, 24, 3576-3587.
PDB codes: 2asb 2atw
16282587 C.D.Borgeson, and M.L.Samson (2005).
Shared RNA-binding sites for interacting members of the Drosophila ELAV family of neuronal proteins.
  Nucleic Acids Res, 33, 6372-6383.  
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.  
16179478 F.C.Oberstrass, S.D.Auweter, M.Erat, Y.Hargous, A.Henning, P.Wenter, L.Reymond, B.Amir-Ahmady, S.Pitsch, D.L.Black, and F.H.Allain (2005).
Structure of PTB bound to RNA: specific binding and implications for splicing regulation.
  Science, 309, 2054-2057.
PDB codes: 2ad9 2adb 2adc
16126720 L.Huang, J.Hwang, S.D.Sharma, M.R.Hargittai, Y.Chen, J.J.Arnold, K.D.Raney, and C.E.Cameron (2005).
Hepatitis C virus nonstructural protein 5A (NS5A) is an RNA-binding protein.
  J Biol Chem, 280, 36417-36428.  
15914668 M.J.Law, E.J.Chambers, P.S.Katsamba, I.S.Haworth, and I.A.Laird-Offringa (2005).
Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction.
  Nucleic Acids Res, 33, 2917-2928.  
16107705 M.Soller, and K.White (2005).
ELAV multimerizes on conserved AU4-6 motifs important for ewg splicing regulation.
  Mol Cell Biol, 25, 7580-7591.  
15809648 P.Gollnick, and A.Antson (2005).
Going for RNA repeats.
  Nat Struct Mol Biol, 12, 289-290.  
16077728 R.Singh, and J.Valcárcel (2005).
Building specificity with nonspecific RNA-binding proteins.
  Nat Struct Mol Biol, 12, 645-653.  
15643449 R.Stefl, L.Skrisovska, and F.H.Allain (2005).
RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle.
  EMBO Rep, 6, 33-38.  
16192572 T.Kumarevel, H.Mizuno, and P.K.Kumar (2005).
Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis.
  Nucleic Acids Res, 33, 5494-5502.
PDB codes: 1wpt 1wrn 1wro
15758992 T.Kumarevel, H.Mizuno, and P.K.Kumar (2005).
Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand.
  Nature, 434, 183-191.
PDB codes: 1wmq 1wps 1wpv
15753311 V.Guallar, and K.W.Borrelli (2005).
A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding.
  Proc Natl Acad Sci U S A, 102, 3954-3959.  
14981510 B.P.Hudson, M.A.Martinez-Yamout, H.J.Dyson, and P.E.Wright (2004).
Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d.
  Nat Struct Mol Biol, 11, 257-264.
PDB code: 1rgo
15004549 C.Alfano, D.Sanfelice, J.Babon, G.Kelly, A.Jacks, S.Curry, and M.R.Conte (2004).
Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein.
  Nat Struct Mol Biol, 11, 323-329.
PDB codes: 1s79 1s7a
15155766 C.Butan, H.Van Der Zandt, and P.A.Tucker (2004).
Structure and assembly of the RNA binding domain of bluetongue virus non-structural protein 2.
  J Biol Chem, 279, 37613-37621.
PDB code: 1uty
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.  
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
15226427 K.L.Carroll, D.A.Pradhan, J.A.Granek, N.D.Clarke, and J.L.Corden (2004).
Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts.
  Mol Cell Biol, 24, 6241-6252.  
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.  
15457527 N.C.Meisner, J.Hackermüller, V.Uhl, A.Aszódi, M.Jaritz, and M.Auer (2004).
mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure.
  Chembiochem, 5, 1432-1447.  
15341728 P.J.Simpson, T.P.Monie, A.Szendröi, N.Davydova, J.K.Tyzack, M.R.Conte, C.M.Read, P.D.Cary, D.I.Svergun, P.V.Konarev, S.Curry, and S.Matthews (2004).
Structure and RNA interactions of the N-terminal RRM domains of PTB.
  Structure, 12, 1631-1643.
PDB codes: 1sjq 1sjr
15299008 Y.Iko, T.S.Kodama, N.Kasai, T.Oyama, E.H.Morita, T.Muto, M.Okumura, R.Fujii, T.Takumi, S.Tate, and K.Morikawa (2004).
Domain architectures and characterization of an RNA-binding protein, TLS.
  J Biol Chem, 279, 44834-44840.  
12781131 C.K.Lau, M.D.Diem, G.Dreyfuss, and G.D.Van Duyne (2003).
Structure of the Y14-Magoh core of the exon junction complex.
  Curr Biol, 13, 933-941.
PDB code: 1p27
12595703 D.B.Hoggan, J.A.Chao, G.S.Prasad, C.D.Stout, and J.R.Williamson (2003).
Combinatorial crystallization of an RNA-protein complex.
  Acta Crystallogr D Biol Crystallogr, 59, 466-473.  
12626338 D.L.Black (2003).
Mechanisms of alternative pre-messenger RNA splicing.
  Annu Rev Biochem, 72, 291-336.  
12912928 D.L.Theobald, and S.C.Schultz (2003).
Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes.
  EMBO J, 22, 4314-4324.
PDB codes: 1pa6 1ph1 1ph2 1ph3 1ph4 1ph5 1ph6 1ph7 1ph8 1ph9 1phj
12809490 G.C.Pérez-Alvarado, M.Martínez-Yamout, M.M.Allen, R.Grosschedl, H.J.Dyson, and P.E.Wright (2003).
Structure of the nuclear factor ALY: insights into post-transcriptional regulatory and mRNA nuclear export processes.
  Biochemistry, 42, 7348-7357.
PDB code: 1no8
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.  
12637517 J.G.De Gaudenzi, I.D'Orso, and A.C.Frasch (2003).
RNA recognition motif-type RNA-binding proteins in Trypanosoma cruzi form a family involved in the interaction with specific transcripts in vivo.
  J Biol Chem, 278, 18884-18894.  
12672694 J.G.Luz, C.A.Hassig, C.Pickle, A.Godzik, B.J.Meyer, and I.A.Wilson (2003).
XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators.
  Genes Dev, 17, 977-990.
PDB code: 1mg7
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
14532129 M.Grskovic, M.W.Hentze, and F.Gebauer (2003).
A co-repressor assembly nucleated by Sex-lethal in the 3'UTR mediates translational control of Drosophila msl-2 mRNA.
  EMBO J, 22, 5571-5581.  
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.  
14602915 T.Ruggiero, M.Olivero, A.Follenzi, L.Naldini, R.Calogero, and M.F.Di Renzo (2003).
Deletion in a (T)8 microsatellite abrogates expression regulation by 3'-UTR.
  Nucleic Acids Res, 31, 6561-6569.  
12637556 U.Kühn, A.Nemeth, S.Meyer, and E.Wahle (2003).
The RNA binding domains of the nuclear poly(A)-binding protein.
  J Biol Chem, 278, 16916-16925.  
11871661 A.Mehta, and D.M.Driscoll (2002).
Identification of domains in apobec-1 complementation factor required for RNA binding and apolipoprotein-B mRNA editing.
  RNA, 8, 69-82.  
12112691 A.Teplyakov, G.Obmolova, M.Tordova, N.Thanki, N.Bonander, E.Eisenstein, A.J.Howard, and G.L.Gilliland (2002).
Crystal structure of the YjeE protein from Haemophilus influenzae: a putative Atpase involved in cell wall synthesis.
  Proteins, 48, 220-226.
PDB codes: 1fl9 1htw
12374755 C.Mazza, A.Segref, I.W.Mattaj, and S.Cusack (2002).
Large-scale induced fit recognition of an m(7)GpppG cap analogue by the human nuclear cap-binding complex.
  EMBO J, 21, 5548-5557.
PDB codes: 1h2t 1h2u 1h2v
12445771 D.D.Boehr, A.R.Farley, G.D.Wright, and J.R.Cox (2002).
Analysis of the pi-pi stacking interactions between the aminoglycoside antibiotic kinase APH(3')-IIIa and its nucleotide ligands.
  Chem Biol, 9, 1209-1217.  
12364610 E.M.Anderson, W.A.Halsey, and D.S.Wuttke (2002).
Delineation of the high-affinity single-stranded telomeric DNA-binding domain of Saccharomyces cerevisiae Cdc13.
  Nucleic Acids Res, 30, 4305-4313.  
12434151 G.Calero, K.F.Wilson, T.Ly, J.L.Rios-Steiner, J.C.Clardy, and R.A.Cerione (2002).
Structural basis of m7GpppG binding to the nuclear cap-binding protein complex.
  Nat Struct Biol, 9, 912-917.
PDB codes: 1n52 1n54
12403777 I.D'Orso, and A.C.Frasch (2002).
TcUBP-1, an mRNA destabilizing factor from trypanosomes, homodimerizes and interacts with novel AU-rich element- and Poly(A)-binding proteins forming a ribonucleoprotein complex.
  J Biol Chem, 277, 50520-50528.  
12466552 J.B.Tuite, J.C.Shiels, and A.M.Baranger (2002).
Substitution of an essential adenine in the U1A-RNA complex with a non-polar isostere.
  Nucleic Acids Res, 30, 5269-5275.  
11788718 J.C.Shiels, J.B.Tuite, S.J.Nolan, and A.M.Baranger (2002).
Investigation of a conserved stacking interaction in target site recognition by the U1A protein.
  Nucleic Acids Res, 30, 550-558.  
11917013 J.Vitali, J.Ding, J.Jiang, Y.Zhang, A.R.Krainer, and R.M.Xu (2002).
Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1.
  Nucleic Acids Res, 30, 1531-1538.
PDB code: 1l3k
11866091 K.Iwasaki, S.Kikukawa, S.Kawamura, Y.Kouzuma, I.Tanaka, and M.Kimura (2002).
On the interaction of ribosomal protein L5 with 5S rRNA.
  Biosci Biotechnol Biochem, 66, 103-109.  
11839493 K.Wild, O.Weichenrieder, K.Strub, I.Sinning, and S.Cusack (2002).
Towards the structure of the mammalian signal recognition particle.
  Curr Opin Struct Biol, 12, 72-81.  
12100721 M.A.Fouraux, A.van der Heijden, W.J.van Venrooij, and G.J.Pruijn (2002).
Cross-reactivity of the anti-La monoclonal antibody SW5 with early endosome antigen 2.
  Immunology, 106, 336-342.  
12093755 M.A.Schumacher, R.F.Pearson, T.Møller, P.Valentin-Hansen, and R.G.Brennan (2002).
Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein.
  EMBO J, 21, 3546-3556.
PDB codes: 1kq1 1kq2
12015979 M.J.Lallena, K.J.Chalmers, S.Llamazares, A.I.Lamond, and J.Valcárcel (2002).
Splicing regulation at the second catalytic step by Sex-lethal involves 3' splice site recognition by SPF45.
  Cell, 109, 285-296.  
12466529 M.Jovanovic, R.Sanchez, S.Altman, and V.Gopalan (2002).
Elucidation of structure-function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach.
  Nucleic Acids Res, 30, 5065-5073.  
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.  
11884397 S.B.Jin, J.Zhao, P.Bjork, K.Schmekel, P.O.Ljungdahl, and L.Wieslander (2002).
Mrd1p is required for processing of pre-rRNA and for maintenance of steady-state levels of 40 S ribosomal subunits in yeast.
  J Biol Chem, 277, 18431-18439.  
12409457 S.Bonnet-Corven, Y.Audic, F.Omilli, and H.B.Osborne (2002).
An analysis of the sequence requirements of EDEN-BP for specific RNA binding.
  Nucleic Acids Res, 30, 4667-4674.  
12121976 S.Horke, K.Reumann, A.Rang, and T.Heise (2002).
Molecular characterization of the human La protein.hepatitis B virus RNA.B interaction in vitro.
  J Biol Chem, 277, 34949-34958.  
11788707 X.Yuan, N.Davydova, M.R.Conte, S.Curry, and S.Matthews (2002).
Chemical shift mapping of RNA interactions with the polypyrimidine tract binding protein.
  Nucleic Acids Res, 30, 456-462.  
11551507 C.L.Kielkopf, N.A.Rodionova, M.R.Green, and S.K.Burley (2001).
A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer.
  Cell, 106, 595-605.
PDB code: 1jmt
11545740 C.Mazza, M.Ohno, A.Segref, I.W.Mattaj, and S.Cusack (2001).
Crystal structure of the human nuclear cap binding complex.
  Mol Cell, 8, 383-396.
PDB code: 1h6k
11514570 G.M.Wilson, K.Sutphen, M.Moutafis, S.Sinha, and G.Brewer (2001).
Structural remodeling of an A + U-rich RNA element by cation or AUF1 binding.
  J Biol Chem, 276, 38400-38409.  
  11560900 G.P.McNeil, A.J.Schroeder, M.A.Roberts, and F.R.Jackson (2001).
Genetic analysis of functional domains within the Drosophila LARK RNA-binding protein.
  Genetics, 159, 229-240.  
11438677 H.Peled-Zehavi, J.A.Berglund, M.Rosbash, and A.D.Frankel (2001).
Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex.
  Mol Cell Biol, 21, 5232-5241.  
11331594 I.Törö, S.Thore, C.Mayer, J.Basquin, B.Séraphin, and D.Suck (2001).
RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex.
  EMBO J, 20, 2293-2303.
PDB codes: 1i4k 1i5l
11179892 J.M.Pérez-Cañadillas, and G.Varani (2001).
Recent advances in RNA-protein recognition.
  Curr Opin Struct Biol, 11, 53-58.  
11463612 J.X.Guo, and W.H.Gmeiner (2001).
Molecular dynamics simulation of the human U2B" protein complex with U2 snRNA hairpin IV in aqueous solution.
  Biophys J, 81, 630-642.  
11238934 L.O.Penalva, M.J.Lallena, and J.Valcárcel (2001).
Switch in 3' splice site recognition between exon definition and splicing catalysis is important for sex-lethal autoregulation.
  Mol Cell Biol, 21, 1986-1996.  
11581160 M.J.Lisbin, J.Qiu, and K.White (2001).
The neuron-specific RNA-binding protein ELAV regulates neuroglian alternative splicing in neurons and binds directly to its pre-mRNA.
  Genes Dev, 15, 2546-2561.  
11134326 R.J.Maraia, and R.V.Intine (2001).
Recognition of nascent RNA by the human La antigen: conserved and divergent features of structure and function.
  Mol Cell Biol, 21, 367-379.  
11139617 S.Jacquenet, D.Ropers, P.S.Bilodeau, L.Damier, A.Mougin, C.M.Stoltzfus, and C.Branlant (2001).
Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing.
  Nucleic Acids Res, 29, 464-478.  
11376140 X.Manival, L.Ghisolfi-Nieto, G.Joseph, P.Bouvet, and M.Erard (2001).
RNA-binding strategies common to cold-shock domain- and RNA recognition motif-containing proteins.
  Nucleic Acids Res, 29, 2223-2233.  
11691992 Z.Liu, I.Luyten, M.J.Bottomley, A.C.Messias, S.Houngninou-Molango, R.Sprangers, K.Zanier, A.Krämer, and M.Sattler (2001).
Structural basis for recognition of the intron branch site RNA by splicing factor 1.
  Science, 294, 1098-1102.
PDB code: 1k1g
10679466 A.A.Antson (2000).
Single-stranded-RNA binding proteins.
  Curr Opin Struct Biol, 10, 87-94.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
11060011 E.Liker, E.Fernandez, E.Izaurralde, and E.Conti (2000).
The structure of the mRNA export factor TAP reveals a cis arrangement of a non-canonical RNP domain and an LRR domain.
  EMBO J, 19, 5587-5598.
PDB codes: 1fo1 1ft8
11118222 F.H.Allain, P.Bouvet, T.Dieckmann, and J.Feigon (2000).
Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin.
  EMBO J, 19, 6870-6881.
PDB code: 1fje
10944102 G.Martin, W.Keller, and S.Doublié (2000).
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.
  EMBO J, 19, 4193-4203.
PDB code: 1f5a
10676814 H.A.Lewis, K.Musunuru, K.B.Jensen, C.Edo, H.Chen, R.B.Darnell, and S.K.Burley (2000).
Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome.
  Cell, 100, 323-332.
PDB code: 1ec6
10801497 L.Jovine, T.Hainzl, C.Oubridge, W.G.Scott, J.Li, T.K.Sixma, A.Wonacott, T.Skarzynski, and K.Nagai (2000).
Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.
  Structure, 8, 527-540.
PDB code: 1duh
10734193 M.Inoue, Y.Muto, H.Sakamoto, and S.Yokoyama (2000).
NMR studies on functional structures of the AU-rich element-binding domains of Hu antigen C.
  Nucleic Acids Res, 28, 1743-1750.
PDB codes: 1d8z 1d9a
  10924474 M.J.Lisbin, M.Gordon, Y.M.Yannoni, and K.White (2000).
Function of RRM domains of Drosophila melanogaster ELAV: Rnp1 mutations and rrm domain replacements with ELAV family proteins and SXL.
  Genetics, 155, 1789-1798.  
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
10753781 P.Mitchell, and D.Tollervey (2000).
mRNA stability in eukaryotes.
  Curr Opin Genet Dev, 10, 193-198.  
10864047 R.Singh, H.Banerjee, and M.R.Green (2000).
Differential recognition of the polypyrimidine-tract by the general splicing factor U2AF65 and the splicing repressor sex-lethal.
  RNA, 6, 901-911.  
10848602 S.Park, D.G.Myszka, M.Yu, S.J.Littler, and I.A.Laird-Offringa (2000).
HuD RNA recognition motifs play distinct roles in the formation of a stable complex with AU-rich RNA.
  Mol Cell Biol, 20, 4765-4772.  
11003644 V.Markovtsov, J.M.Nikolic, J.A.Goldman, C.W.Turck, M.Y.Chou, and D.L.Black (2000).
Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein.
  Mol Cell Biol, 20, 7463-7479.  
  10791828 V.Sievert, S.Kuhn, A.Paululat, and W.Traut (2000).
Sequence conservation and expression of the sex-lethal homologue in the fly Megaselia scalaris.
  Genome, 43, 382-390.  
10660288 Y.Muto, C.Oubridge, and K.Nagai (2000).
RNA-binding proteins: TRAPping RNA bases.
  Curr Biol, 10, R19-R21.  
10545124 F.Gebauer, D.F.Corona, T.Preiss, P.B.Becker, and M.W.Hentze (1999).
Translational control of dosage compensation in Drosophila by Sex-lethal: cooperative silencing via the 5' and 3' UTRs of msl-2 mRNA is independent of the poly(A) tail.
  EMBO J, 18, 6146-6154.  
10573119 M.B.Elliott, P.A.Gottlieb, and P.Gollnick (1999).
Probing the TRAP-RNA interaction with nucleoside analogs.
  RNA, 5, 1277-1289.  
10499800 R.C.Deo, J.B.Bonanno, N.Sonenberg, and S.K.Burley (1999).
Recognition of polyadenylate RNA by the poly(A)-binding protein.
  Cell, 98, 835-845.
PDB code: 1cvj
10449418 T.Ito, Y.Muto, M.R.Green, and S.Yokoyama (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.
PDB codes: 1u2f 2u2f
  10490595 V.A.Raker, K.Hartmuth, B.Kastner, and R.Lührmann (1999).
Spliceosomal U snRNP core assembly: Sm proteins assemble onto an Sm site RNA nonanucleotide in a specific and thermodynamically stable manner.
  Mol Cell Biol, 19, 6554-6565.  
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