spacer
spacer

PDBsum entry 1a9n

Go to PDB code: 
protein dna_rna Protein-protein interface(s) links
RNA binding protein/RNA PDB id
1a9n
Jmol
Contents
Protein chains
162 a.a. *
174 a.a. *
94 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1a9n
Name: RNA binding protein/RNA
Title: Crystal structure of the spliceosomal u2b''-u2a' protein complex bound to a fragment of u2 small nuclear RNA
Structure: RNA (5'- r( Cp Cp Up Gp Gp Up Ap Up Up Gp Cp Ap Gp Up Ap Cp Cp Up Cp Cp Ap Gp Gp U)-3'). Chain: q, r. Fragment: u2 hairpin iv. Engineered: yes. U2a'. Chain: a, c. Fragment: n-terminal domain, residues 1 - 176 of u2 a', a
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: cdna clone. Other_details: cdna clone
Biol. unit: Trimer (from PQS)
Resolution:
2.38Å     R-factor:   0.282     R-free:   0.328
Authors: S.R.Price,P.R.Evans,K.Nagai
Key ref:
S.R.Price et al. (1998). Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA. Nature, 394, 645-650. PubMed id: 9716128 DOI: 10.1038/29234
Date:
08-Apr-98     Release date:   23-Sep-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09661  (RU2A_HUMAN) -  U2 small nuclear ribonucleoprotein A'
Seq:
Struc:
255 a.a.
162 a.a.*
Protein chain
Pfam   ArchSchema ?
P09661  (RU2A_HUMAN) -  U2 small nuclear ribonucleoprotein A'
Seq:
Struc:
255 a.a.
174 a.a.*
Protein chains
Pfam   ArchSchema ?
P08579  (RU2B_HUMAN) -  U2 small nuclear ribonucleoprotein B''
Seq:
Struc:
225 a.a.
94 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nuclear mRNA splicing, via spliceosome   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1038/29234 Nature 394:645-650 (1998)
PubMed id: 9716128  
 
 
Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA.
S.R.Price, P.R.Evans, K.Nagai.
 
  ABSTRACT  
 
We have determined the crystal structure at 2.4 A resolution of a ternary complex between the spliceosomal U2B"/U2A' protein complex and hairpin-loop IV of U2 small nuclear RNA. Unlike its close homologue the U1A protein, U2B" binds to its cognate RNA only in the presence of U2A', which contains leucine-rich repeats in its sequence. The concave surface of a parallel beta-sheet within the leucine-rich-repeat region of U2A' interacts with the ribonucleoprotein domain of U2B" on the surface opposite its RNA-binding surface. The basic carboxy-terminal region of U2A' interacts with the RNA stem. The crystal structure reveals how protein-protein interaction regulates RNA-binding specificity, and how replacing only a few key residues allows the U2B" and U1A proteins to discriminate between their cognate RNA hairpins by forming alternative networks of interactions.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Comparison of the RNA-protein interfaces between the U2B"/U2LRR(U2A')/RNA complex and the U1A protein-RNA complex10. a, Stacking and hydrogen-bonding interactions of C10, A11 and G12 in the U2B"/U2LRR/RNA complex; b, the stepladder structure with three stacked nucleotide bases, A14, C15 and C16; c, the hydrogen-bonding interactions of the loop-closing C5 G16 base pair in the U1A-RNA complex10; d, the intricate hydrogen-bonding interactions of the loop-closing U5 U17 base pair in the U2B"/U2A'/RNA complex. e, The hydrogen-bonding network of U7, G9 and Glu 19 in the U1A-RNA complex10; f, the hydrogen-bonding network of U7, G9, Asp 19 and Arg 52 in the U2B"/U2LRR/RNA complex. These figures are drawn using Bobscript50.
Figure 4.
Figure 4 Interaction between U2A' (U2 LRR) protein and the RNA stem in the U2B"/U2LRR/RNA and hypothetical U1A/U2LRR/RNA complexes. a, A surface representation49 of the U2B"/U2A'(U2LRR)/RNA complex with electrostatic potential. Blue, positive; red, negative. b, A surface representation of the U2B"/U2LRR/RNA complex showing the interaction between U2LRR protein and the RNA stem. c, A model of a complex between U2LRR protein and the U1A-RNA complex10 generated by computer graphics docking. The surface is colour-coded as in Fig. 2c, d.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 394, 645-650) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
21822283 M.Teplova, L.Wohlbold, N.W.Khin, E.Izaurralde, and D.J.Patel (2011).
Structure-function studies of nucleocytoplasmic transport of retroviral genomic RNA by mRNA export factor TAP.
  Nat Struct Mol Biol, 18, 990-998.
PDB codes: 3rw6 3rw7
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.  
19838329 J.G.Routsias, N.Kyriakidis, M.Latreille, and A.G.Tzioufas (2010).
RNA recognition motif (RRM) of La/SSB: the bridge for interparticle spreading of autoimmune response to U1-RNP.
  Mol Med, 16, 19-26.  
  19927321 K.K.Singarapu, J.L.Mills, R.Xiao, T.Acton, M.Punta, M.Fischer, B.Honig, B.Rost, G.T.Montelione, and T.Szyperski (2010).
Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175.
  Proteins, 78, 779-784.
PDB codes: 2jz5 2k3i
19447915 C.Netter, G.Weber, H.Benecke, and M.C.Wahl (2009).
Functional stabilization of an RNA recognition motif by a noncanonical N-terminal expansion.
  RNA, 15, 1305-1313.
PDB code: 3egn
19542313 C.Preusser, Z.Palfi, and A.Bindereif (2009).
Special Sm core complex functions in assembly of the U2 small nuclear ribonucleoprotein of Trypanosoma brucei.
  Eukaryot Cell, 8, 1228-1234.  
19325628 D.A.Pomeranz Krummel, C.Oubridge, A.K.Leung, J.Li, and K.Nagai (2009).
Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.
  Nature, 458, 475-480.
PDB code: 3cw1
19173316 D.Das, P.Kozbial, H.L.Axelrod, M.D.Miller, D.McMullan, S.S.Krishna, P.Abdubek, C.Acosta, T.Astakhova, P.Burra, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, Y.Elias, M.A.Elsliger, D.Ernst, C.Farr, J.Feuerhelm, A.Grzechnik, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, A.Kumar, D.Marciano, A.T.Morse, K.D.Murphy, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, S.Sudek, H.Tien, C.Trame, C.V.Trout, H.van den Bedem, D.Weekes, A.White, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.
  Proteins, 75, 296-307.
PDB code: 3by7
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
19452560 K.L.Hindle, J.Bella, and S.C.Lovell (2009).
Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.
  Proteins, 77, 342-358.  
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.  
18410380 C.de Chiara, R.P.Menon, and A.Pastore (2008).
Structural bases for recognition of Anp32/LANP proteins.
  FEBS J, 275, 2548-2560.
PDB code: 2jqd
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.  
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
19077264 H.Park, J.Huxley-Jones, R.P.Boot-Handford, P.N.Bishop, T.K.Attwood, and J.Bella (2008).
LRRCE: a leucine-rich repeat cysteine capping motif unique to the chordate lineage.
  BMC Genomics, 9, 599.  
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
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.  
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
17978099 L.H.Matzat, S.Berberoglu, and L.Lévesque (2008).
Formation of a Tap/NXF1 Homotypic Complex Is Mediated through the Amino-Terminal Domain of Tap and Enhances Interaction with Nucleoporins.
  Mol Biol Cell, 19, 327-338.  
18446235 M.Proell, S.J.Riedl, J.H.Fritz, A.M.Rojas, and R.Schwarzenbacher (2008).
The Nod-like receptor (NLR) family: a tale of similarities and differences.
  PLoS ONE, 3, e2119.  
18214954 Q.R.Fan, and W.A.Hendrickson (2008).
Comparative structural analysis of the binding domain of follicle stimulating hormone receptor.
  Proteins, 72, 393-401.  
17506639 A.Cook, F.Bono, M.Jinek, and E.Conti (2007).
Structural biology of nucleocytoplasmic transport.
  Annu Rev Biochem, 76, 647-671.  
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.  
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
17475252 L.Pérez-Díaz, M.A.Duhagon, P.Smircich, J.Sotelo-Silveira, C.Robello, M.A.Krieger, S.Goldenberg, N.Williams, B.Dallagiovanna, and B.Garat (2007).
Trypanosoma cruzi: molecular characterization of an RNA binding protein differentially expressed in the parasite life cycle.
  Exp Parasitol, 117, 99.  
17360628 M.D.Ohi, L.Ren, J.S.Wall, K.L.Gould, and T.Walz (2007).
Structural characterization of the fission yeast U5.U2/U6 spliceosome complex.
  Proc Natl Acad Sci U S A, 104, 3195-3200.  
17517123 N.Matsushima, T.Tanaka, P.Enkhbayar, T.Mikami, M.Taga, K.Yamada, and Y.Kuroki (2007).
Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors.
  BMC Genomics, 8, 124.  
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.  
17567741 T.Huyton, and C.Wolberger (2007).
The crystal structure of the tumor suppressor protein pp32 (Anp32a): structural insights into Anp32 family of proteins.
  Protein Sci, 16, 1308-1315.
PDB codes: 2je0 2je1
17535930 T.Saldi, C.Wilusz, M.MacMorris, and T.Blumenthal (2007).
Functional redundancy of worm spliceosomal proteins U1A and U2B''.
  Proc Natl Acad Sci U S A, 104, 9753-9757.  
17881380 T.V.Aspinall, J.M.Gordon, H.J.Bennett, P.Karahalios, J.P.Bukowski, S.C.Walker, D.R.Engelke, and J.M.Avis (2007).
Interactions between subunits of Saccharomyces cerevisiae RNase MRP support a conserved eukaryotic RNase P/MRP architecture.
  Nucleic Acids Res, 35, 6439-6450.  
17643112 Y.Kotake, K.Sagane, T.Owa, Y.Mimori-Kiyosue, H.Shimizu, M.Uesugi, Y.Ishihama, M.Iwata, and Y.Mizui (2007).
Splicing factor SF3b as a target of the antitumor natural product pladienolide.
  Nat Chem Biol, 3, 570-575.  
16689644 H.Stark, and R.Lührmann (2006).
Cryo-electron microscopy of spliceosomal components.
  Annu Rev Biophys Biomol Struct, 35, 435-457.  
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.  
17098193 K.Kuwasako, F.He, M.Inoue, A.Tanaka, S.Sugano, P.Güntert, Y.Muto, and S.Yokoyama (2006).
Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP.
  Structure, 14, 1677-1689.
PDB codes: 2dt6 2dt7
16406303 L.Federici, A.Di Matteo, J.Fernandez-Recio, D.Tsernoglou, and F.Cervone (2006).
Polygalacturonase inhibiting proteins: players in plant innate immunity?
  Trends Plant Sci, 11, 65-70.  
16537922 O.Dybkov, C.L.Will, J.Deckert, N.Behzadnia, K.Hartmuth, and R.Lührmann (2006).
U2 snRNA-protein contacts in purified human 17S U2 snRNPs and in spliceosomal A and B complexes.
  Mol Cell Biol, 26, 2803-2816.  
16679019 S.Curry, and M.R.Conte (2006).
A terminal affair: 3'-end recognition by the human La protein.
  Trends Biochem Sci, 31, 303-305.  
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
16629662 W.Daher, E.Browaeys, C.Pierrot, H.Jouin, D.Dive, E.Meurice, C.Dissous, M.Capron, S.Tomavo, C.Doerig, K.Cailliau, and J.Khalife (2006).
Regulation of protein phosphatase type 1 and cell cycle progression by PfLRR1, a novel leucine-rich repeat protein of the human malaria parasite Plasmodium falciparum.
  Mol Microbiol, 60, 578-590.  
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.  
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.  
16209941 B.Hao, N.Zheng, B.A.Schulman, G.Wu, J.J.Miller, M.Pagano, and N.P.Pavletich (2005).
Structural basis of the Cks1-dependent recognition of p27(Kip1) by the SCF(Skp2) ubiquitin ligase.
  Mol Cell, 20, 9.
PDB codes: 2ass 2ast
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.  
16096647 H.Benecke, R.Lührmann, and C.L.Will (2005).
The U11/U12 snRNP 65K protein acts as a molecular bridge, binding the U12 snRNA and U11-59K protein.
  EMBO J, 24, 3057-3069.  
16164979 K.A.Dickson, M.C.Haigis, and R.T.Raines (2005).
Ribonuclease inhibitor: structure and function.
  Prog Nucleic Acid Res Mol Biol, 80, 349-374.  
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.  
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.  
  16511018 T.Jin, A.J.Howard, E.A.Golemis, Y.Wang, and Y.Z.Zhang (2005).
Overproduction, purification, crystallization and preliminary X-ray diffraction studies of the human spliceosomal protein TXNL4B.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 282-284.  
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.  
14734555 L.B.Clark, P.Viswanathan, G.Quigley, Y.C.Chiang, J.S.McMahon, G.Yao, J.Chen, A.Nelsbach, and C.L.Denis (2004).
Systematic mutagenesis of the leucine-rich repeat (LRR) domain of CCR4 reveals specific sites for binding to CAF1 and a separate critical role for the LRR in CCR4 deadenylase activity.
  J Biol Chem, 279, 13616-13623.  
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.  
14747988 P.Enkhbayar, M.Kamiya, M.Osaki, T.Matsumoto, and N.Matsushima (2004).
Structural principles of leucine-rich repeat (LRR) proteins.
  Proteins, 54, 394-403.  
15121895 P.S.Klosterman, D.K.Hendrix, M.Tamura, S.R.Holbrook, and S.E.Brenner (2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
  Nucleic Acids Res, 32, 2342-2352.  
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.  
15211521 S.Lu, J.Symersky, S.Li, M.Carson, L.Chen, E.Meehan, and M.Luo (2004).
Structural genomics of Caenorhabditis elegans: crystal structure of the tropomodulin C-terminal domain.
  Proteins, 56, 384-386.
PDB code: 1pgv
15044951 T.Tanabe, M.Chamaillard, Y.Ogura, L.Zhu, S.Qiu, J.Masumoto, P.Ghosh, A.Moran, M.M.Predergast, G.Tromp, C.J.Williams, N.Inohara, and G.Núñez (2004).
Regulatory regions and critical residues of NOD2 involved in muramyl dipeptide recognition.
  EMBO J, 23, 1587-1597.  
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.  
12904578 A.Di Matteo, L.Federici, B.Mattei, G.Salvi, K.A.Johnson, C.Savino, G.De Lorenzo, D.Tsernoglou, and F.Cervone (2003).
The crystal structure of polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein involved in plant defense.
  Proc Natl Acad Sci U S A, 100, 10124-10128.
PDB code: 1ogq
12540576 E.Skrzypek, T.Myers-Morales, S.W.Whiteheart, and S.C.Straley (2003).
Application of a Saccharomyces cerevisiae model to study requirements for trafficking of Yersinia pestis YopM in eucaryotic cells.
  Infect Immun, 71, 937-947.  
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
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
12601689 H.Wu, and S.M.King (2003).
Backbone dynamics of dynein light chains.
  Cell Motil Cytoskeleton, 54, 267-273.  
12824344 H.Yang, F.Jossinet, N.Leontis, L.Chen, J.Westbrook, H.Berman, and E.Westhof (2003).
Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
12851400 J.Gallego, J.Greatorex, H.Zhang, B.Yang, S.Arunachalam, J.Fang, J.Seamons, S.Lea, R.J.Pomerantz, and A.M.Lever (2003).
Rev binds specifically to a purine loop in the SL1 region of the HIV-1 leader RNA.
  J Biol Chem, 278, 40385-40391.  
12791136 M.P.Machner, S.Frese, W.D.Schubert, V.Orian-Rousseau, E.Gherardi, J.Wehland, H.H.Niemann, and D.W.Heinz (2003).
Aromatic amino acids at the surface of InlB are essential for host cell invasion by Listeria monocytogenes.
  Mol Microbiol, 48, 1525-1536.  
12590136 P.Viswanathan, J.Chen, Y.C.Chiang, and C.L.Denis (2003).
Identification of multiple RNA features that influence CCR4 deadenylation activity.
  J Biol Chem, 278, 14949-14955.  
12925992 Q.Vicens, and E.Westhof (2003).
Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures.
  Biopolymers, 70, 42-57.  
12540850 R.Pudi, S.Abhiman, N.Srinivasan, and S.Das (2003).
Hepatitis C virus internal ribosome entry site-mediated translation is stimulated by specific interaction of independent regions of human La autoantigen.
  J Biol Chem, 278, 12231-12240.  
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
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.  
12191478 A.B.Hickman, D.R.Ronning, R.M.Kotin, and F.Dyda (2002).
Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep.
  Mol Cell, 10, 327-337.
PDB code: 1m55
11967365 A.V.Kajava, and B.Kobe (2002).
Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information.
  Protein Sci, 11, 1082-1090.  
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.  
11854490 D.N.Ho, G.A.Coburn, Y.Kang, B.R.Cullen, and M.M.Georgiadis (2002).
The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor.
  Proc Natl Acad Sci U S A, 99, 1888-1893.
PDB codes: 1koh 1koo
12226088 H.Ceulemans, V.Vulsteke, M.De Maeyer, K.Tatchell, W.Stalmans, and M.Bollen (2002).
Binding of the concave surface of the Sds22 superhelix to the alpha 4/alpha 5/alpha 6-triangle of protein phosphatase-1.
  J Biol Chem, 277, 47331-47337.  
11700323 H.D.Cho, K.Tomita, T.Suzuki, and A.M.Weiner (2002).
U2 small nuclear RNA is a substrate for the CCA-adding enzyme (tRNA nucleotidyltransferase).
  J Biol Chem, 277, 3447-3455.  
12414704 I.Krieger, A.Kostyukova, A.Yamashita, Y.Nitanai, and Y.Maéda (2002).
Crystal structure of the C-terminal half of tropomodulin and structural basis of actin filament pointed-end capping.
  Biophys J, 83, 2716-2725.
PDB code: 1io0
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.  
12213767 M.Mondragón-Palomino, B.C.Meyers, R.W.Michelmore, and B.S.Gaut (2002).
Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana.
  Genome Res, 12, 1305-1315.  
11991638 M.S.Jurica, L.J.Licklider, S.R.Gygi, N.Grigorieff, and M.J.Moore (2002).
Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis.
  RNA, 8, 426-439.  
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.  
12087105 S.Uff, J.M.Clemetson, T.Harrison, K.J.Clemetson, and J.Emsley (2002).
Crystal structure of the platelet glycoprotein Ib(alpha) N-terminal domain reveals an unmasking mechanism for receptor activation.
  J Biol Chem, 277, 35657-35663.
PDB code: 1gwb
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.  
11557816 A.A.Nagengast, and H.K.Salz (2001).
The Drosophila U2 snRNP protein U2A' has an essential function that is SNF/U2B" independent.
  Nucleic Acids Res, 29, 3841-3847.  
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
11504559 C.W.Ward, and T.P.Garrett (2001).
The relationship between the L1 and L2 domains of the insulin and epidermal growth factor receptors and leucine-rich repeat modules.
  BMC Bioinformatics, 2, 4.  
11358864 G.A.Coburn, H.L.Wiegand, Y.Kang, D.N.Ho, M.M.Georgiadis, and B.R.Cullen (2001).
Using viral species specificity to define a critical protein/RNA interaction surface.
  Genes Dev, 15, 1194-1205.  
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.  
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.  
11606722 S.Danner, and J.G.Belasco (2001).
T7 phage display: a novel genetic selection system for cloning RNA-binding proteins from cDNA libraries.
  Proc Natl Acad Sci U S A, 98, 12954-12959.  
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.  
11050437 B.Kobe, and A.V.Kajava (2000).
When protein folding is simplified to protein coiling: the continuum of solenoid protein structures.
  Trends Biochem Sci, 25, 509-515.  
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
10745007 H.Zhang, M.C.Seabra, and J.Deisenhofer (2000).
Crystal structure of Rab geranylgeranyltransferase at 2.0 A resolution.
  Structure, 8, 241-251.
PDB code: 1dce
10688667 J.M.Klein Gunnewiek, R.I.Hussein, Y.van Aarssen, D.Palacios, R.de Jong, W.J.van Venrooij, and S.I.Gunderson (2000).
Fourteen residues of the U1 snRNP-specific U1A protein are required for homodimerization, cooperative RNA binding, and inhibition of polyadenylation.
  Mol Cell Biol, 20, 2209-2217.  
10944346 L.Jovine, T.Hainz, C.Oubridge, and K.Nagai (2000).
Crystallization and preliminary X-ray analysis of the conserved domain IV of Escherichia coli 4.5S RNA.
  Acta Crystallogr D Biol Crystallogr, 56, 1033-1037.  
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
  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.  
10922035 M.Marino, L.Braun, P.Cossart, and P.Ghosh (2000).
A framework for interpreting the leucine-rich repeats of the Listeria internalins.
  Proc Natl Acad Sci U S A, 97, 8784-8788.  
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
10656267 N.Matsushima, T.Ohyanagi, T.Tanaka, and R.H.Kretsinger (2000).
Super-motifs and evolution of tandem leucine-rich repeats within the small proteoglycans--biglycan, decorin, lumican, fibromodulin, PRELP, keratocan, osteoadherin, epiphycan, and osteoglycin.
  Proteins, 38, 210-225.  
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.  
10385517 A.Krämer, P.Grüter, K.Gröning, and B.Kastner (1999).
Combined biochemical and electron microscopic analyses reveal the architecture of the mammalian U2 snRNP.
  J Cell Biol, 145, 1355-1368.  
10378263 B.Kobe, T.Gleichmann, J.Horne, I.G.Jennings, P.D.Scotney, and T.Teh (1999).
Turn up the HEAT.
  Structure, 7, R91-R97.  
10025403 C.Kambach, S.Walke, R.Young, J.M.Avis, E.de la Fortelle, V.A.Raker, R.Lührmann, J.Li, and K.Nagai (1999).
Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs.
  Cell, 96, 375-387.
PDB codes: 1b34 1d3b
10368286 H.A.Lewis, H.Chen, C.Edo, R.J.Buckanovich, Y.Y.Yang, K.Musunuru, R.Zhong, R.B.Darnell, and S.K.Burley (1999).
Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains.
  Structure, 7, 191-203.
PDB codes: 1dt4 1dtj
  10323862 J.Ding, M.K.Hayashi, Y.Zhang, L.Manche, A.R.Krainer, and R.M.Xu (1999).
Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA.
  Genes Dev, 13, 1102-1115.
PDB code: 2up1
10089325 K.Reuter, and R.Ficner (1999).
Overproduction, purification, crystallization and preliminary x-ray diffraction studies of the human spliceosomal protein U5-15kD.
  Acta Crystallogr D Biol Crystallogr, 55, 888-890.  
10635330 M.Marino, L.Braun, P.Cossart, and P.Ghosh (1999).
Structure of the lnlB leucine-rich repeats, a domain that triggers host cell invasion by the bacterial pathogen L. monocytogenes.
  Mol Cell, 4, 1063-1072.
PDB code: 1d0b
10562563 M.Stoldt, J.Wöhnert, O.Ohlenschläger, M.Görlach, and L.R.Brown (1999).
The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.
  EMBO J, 18, 6508-6521.
PDB code: 1d6k
  10072385 O.Puig, A.Gottschalk, P.Fabrizio, and B.Séraphin (1999).
Interaction of the U1 snRNP with nonconserved intronic sequences affects 5' splice site selection.
  Genes Dev, 13, 569-580.  
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
10394366 R.C.Hillig, L.Renault, I.R.Vetter, T.Drell, A.Wittinghofer, and J.Becker (1999).
The crystal structure of rna1p: a new fold for a GTPase-activating protein.
  Mol Cell, 3, 781-791.
PDB code: 1yrg
  10545453 R.M.Vidaver, D.M.Fortner, L.S.Loos-Austin, and D.A.Brow (1999).
Multiple functions of Saccharomyces cerevisiae splicing protein Prp24 in U6 RNA structural rearrangements.
  Genetics, 153, 1205-1218.  
10400475 S.Cusack (1999).
RNA-protein complexes.
  Curr Opin Struct Biol, 9, 66-73.  
10608840 S.G.Schaaf, J.Beck, and M.Nassal (1999).
A small 2'-OH- and base-dependent recognition element downstream of the initiation site in the RNA encapsidation signal is essential for hepatitis B virus replication initiation.
  J Biol Chem, 274, 37787-37794.  
10220389 S.M.Crowder, R.Kanaar, D.C.Rio, and T.Alber (1999).
Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal.
  Proc Natl Acad Sci U S A, 96, 4892-4897.
PDB code: 3sxl
10580472 S.M.Stitzinger, T.R.Conrad, A.M.Zachlin, and H.K.Salz (1999).
Functional analysis of SNF, the Drosophila U1A/U2B" homolog: identification of dispensable and indispensable motifs for both snRNP assembly and function in vivo.
  RNA, 5, 1440-1450.  
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
10333740 D.J.Patel (1998).
Molecular insights into the RNA world.
  Biopolymers, 48, 97.  
9799242 F.Caspary, and B.Séraphin (1998).
The yeast U2A'/U2B complex is required for pre-spliceosome formation.
  EMBO J, 17, 6348-6358.  
9814759 M.E.Rimmele, and J.G.Belasco (1998).
Target discrimination by RNA-binding proteins: role of the ancillary protein U2A' and a critical leucine residue in differentiating the RNA-binding specificity of spliceosomal proteins U1A and U2B".
  RNA, 4, 1386-1396.  
9875850 M.P.Horvath, V.L.Schweiker, J.M.Bevilacqua, J.A.Ruggles, and S.C.Schultz (1998).
Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA.
  Cell, 95, 963-974.
PDB code: 1otc
10333745 R.N.De Guzman, R.B.Turner, and M.F.Summers (1998).
Protein-RNA recognition.
  Biopolymers, 48, 181-195.  
9860948 S.Niranjanakumari, T.Stams, S.M.Crary, D.W.Christianson, and C.A.Fierke (1998).
Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA.
  Proc Natl Acad Sci U S A, 95, 15212-15217.  
9914252 W.G.Scott (1998).
RNA catalysis.
  Curr Opin Struct Biol, 8, 720-726.  
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.