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PDBsum entry 1ec6
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protein dna_rna Protein-protein interface(s) links
RNA binding protein/RNA PDB id
1ec6

 

 

 

 

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Contents
Protein chains
87 a.a. *
DNA/RNA
Waters ×170
* Residue conservation analysis
PDB id:
1ec6
Name: RNA binding protein/RNA
Title: Crystal structure of nova-2 kh3 k-homology RNA-binding domain bound to 20-mer RNA hairpin
Structure: 20-mer RNA hairpin. Chain: c, d. Engineered: yes. RNA-binding protein nova-2. Chain: a, b. Fragment: kh3. Synonym: astrocytic nova-like RNA-binding protein. Engineered: yes
Source: Synthetic: yes. Other_details: product of selex protein binding study. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.208     R-free:   0.291
Authors: H.A.Lewis,K.Musunuru,K.B.Jensen,C.Edo,H.Chen
Key ref:
H.A.Lewis et al. (2000). Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Cell, 100, 323-332. PubMed id: 10676814 DOI: 10.1016/S0092-8674(00)80668-6
Date:
25-Jan-00     Release date:   21-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9UNW9  (NOVA2_HUMAN) -  RNA-binding protein Nova-2 from Homo sapiens
Seq:
Struc: 		492 a.a.
87 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  G-A-G-G-A-C-C-U-A-G-A-U-C-A-C-C-C-C-U-C 20 bases
  G-A-G-G-A-C-C-U-A-G-A-U-C-A-C-C-C-C-U-C 20 bases

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/S0092-8674(00)80668-6 Cell 100:323-332 (2000)
PubMed id: 10676814  
 
 
Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome.
H.A.Lewis, K.Musunuru, K.B.Jensen, C.Edo, H.Chen, R.B.Darnell, S.K.Burley.
 
  ABSTRACT  
 
The structure of a Nova protein K homology (KH) domain recognizing single-stranded RNA has been determined at 2.4 A resolution. Mammalian Nova antigens (1 and 2) constitute an important family of regulators of RNA metabolism in neurons, first identified using sera from cancer patients with the autoimmune disorder paraneoplastic opsoclonus-myoclonus ataxia (POMA). The structure of the third KH domain (KH3) of Nova-2 bound to a stem loop RNA resembles a molecular vise, with 5'-Ura-Cyt-Ade-Cyt-3' pinioned between an invariant Gly-X-X-Gly motif and the variable loop. Tetranucleotide recognition is supported by an aliphatic alpha helix/beta sheet RNA-binding platform, which mimics 5'-Ura-Gua-3' by making Watson-Crick-like hydrogen bonds with 5'-Cyt-Ade-3'. Sequence conservation suggests that fragile X mental retardation results from perturbation of RNA binding by the FMR1 protein.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stem Loop RNA StructuresSchematic drawings of the stem loop crystallization RNAs in complexes 1 and 2. Nucleotides making direct protein contacts are denoted with *. Color coding denotes nucleotides making extensive protein contacts (Ade-11 through Cyt-15; magenta, pink, gold, green, and blue) and the remaining nucleotides (gray). 		Figure 5.
Figure 5. 5′-Ura-Cyt-Ade-Cyt-3′ Binding by Nova-2 KH3RIBBONS drawings showing the RNA-binding surface sandwiched between the invariant Gly-X-X-Gly motif (yellow) and the variable loop (red). The portion of the stem loop crystallization RNA making extensive protein contacts has been included as a color-coded stick figure (Figure 2) with the aliphatic residues (gray) comprising the hydrophobic α/β RNA binding platform. (A) shows the entire complex. (B), (C), and (D) show the environments of Ade-11 Ura-12, and Cyt-13, respectively. (E) shows the environments of Ade-14 and Cyt-15. The side chain of Leu-28 is denoted with *. (F) corresponds to the views used in (D) and (E), with the overlying RNA removed, and shows the aliphatic platform with the jaws of the molecular vise.
 
  The above figures are reprinted by permission from Cell Press: Cell (2000, 100, 323-332) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23142982 G.Nicastro, M.F.García-Mayoral, D.Hollingworth, G.Kelly, S.R.Martin, P.Briata, R.Gherzi, and A.Ramos (2012).
Noncanonical G recognition mediates KSRP regulation of let-7 biogenesis.
  Nat Struct Mol Biol, 19, 1282-1286.
PDB code: 4b8t
21241883 C.Dominguez, M.Schubert, O.Duss, S.Ravindranathan, and F.H.Allain (2011).
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy.
  Prog Nucl Magn Reson Spectrosc, 58, 1.  
20584894 A.Chaudhury, P.Chander, and P.H.Howe (2010).
Heterogeneous nuclear ribonucleoproteins (hnRNPs) in cellular processes: Focus on hnRNP E1's multifunctional regulatory roles.
  RNA, 16, 1449-1462.  
20223220 C.Beuck, B.R.Szymczyna, D.E.Kerkow, A.B.Carmel, L.Columbus, R.L.Stanfield, and J.R.Williamson (2010).
Structure of the GLD-1 homodimerization domain: insights into STAR protein-mediated translational regulation.
  Structure, 18, 377-389.
PDB codes: 3k6t 3kbl
20668163 C.Cai, K.Tamai, and K.Molyneaux (2010).
KHDC1B is a novel CPEB binding partner specifically expressed in mouse oocytes and early embryos.
  Mol Biol Cell, 21, 3137-3148.  
20385598 I.Díaz-Moreno, D.Hollingworth, G.Kelly, S.Martin, M.García-Mayoral, P.Briata, R.Gherzi, and A.Ramos (2010).
Orientation of the central domains of KSRP and its implications for the interaction with the RNA targets.
  Nucleic Acids Res, 38, 5193-5205.  
20080952 J.A.Chao, Y.Patskovsky, V.Patel, M.Levy, S.C.Almo, and R.H.Singer (2010).
ZBP1 recognition of beta-actin zipcode induces RNA looping.
  Genes Dev, 24, 148-158.
PDB code: 3krm
20382833 J.J.Wolf, R.D.Dowell, S.Mahony, M.Rabani, D.K.Gifford, and G.R.Fink (2010).
Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast.
  Genetics, 185, 513-522.  
20948916 R.B.Darnell (2010).
RNA regulation in neurologic disease and cancer.
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19457263 A.Galarneau, and S.Richard (2009).
The STAR RNA binding proteins GLD-1, QKI, SAM68 and SLM-2 bind bipartite RNA motifs.
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19706445 C.Tu, X.Zhou, J.E.Tropea, B.P.Austin, D.S.Waugh, D.L.Court, and X.Ji (2009).
Structure of ERA in complex with the 3' end of 16S rRNA: implications for ribosome biogenesis.
  Proc Natl Acad Sci U S A, 106, 14843-14848.
PDB codes: 3ieu 3iev
19646450 D.E.Kim, B.Blum, P.Bradley, and D.Baker (2009).
Sampling bottlenecks in de novo protein structure prediction.
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19304800 F.E.Loughlin, R.E.Mansfield, P.M.Vaz, A.P.McGrath, S.Setiyaputra, R.Gamsjaeger, E.S.Chen, B.J.Morris, J.M.Guss, and J.P.Mackay (2009).
The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences.
  Proc Natl Acad Sci U S A, 106, 5581-5586.
PDB code: 3g9y
19198587 I.Díaz-Moreno, D.Hollingworth, T.A.Frenkiel, G.Kelly, S.Martin, S.Howell, M.García-Mayoral, R.Gherzi, P.Briata, and A.Ramos (2009).
Phosphorylation-mediated unfolding of a KH domain regulates KSRP localization via 14-3-3 binding.
  Nat Struct Mol Biol, 16, 238-246.
PDB code: 2opu
20011099 J.B.Zang, E.D.Nosyreva, C.M.Spencer, L.J.Volk, K.Musunuru, R.Zhong, E.F.Stone, L.A.Yuva-Paylor, K.M.Huber, R.Paylor, J.C.Darnell, and R.B.Darnell (2009).
A mouse model of the human Fragile X syndrome I304N mutation.
  PLoS Genet, 5, e1000758.  
19487368 J.C.Darnell, C.E.Fraser, O.Mostovetsky, and R.B.Darnell (2009).
Discrimination of common and unique RNA-binding activities among Fragile X mental retardation protein paralogs.
  Hum Mol Genet, 18, 3164-3177.  
19915141 J.M.Pagano, B.M.Farley, K.I.Essien, and S.P.Ryder (2009).
RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3.
  Proc Natl Acad Sci U S A, 106, 20252-20257.  
19221030 M.Ruggiu, R.Herbst, N.Kim, M.Jevsek, J.J.Fak, M.A.Mann, G.Fischbach, S.J.Burden, and R.B.Darnell (2009).
Rescuing Z+ agrin splicing in Nova null mice restores synapse formation and unmasks a physiologic defect in motor neuron firing.
  Proc Natl Acad Sci U S A, 106, 3513-3518.  
19828617 P.Serrano, M.A.Johnson, A.Chatterjee, B.W.Neuman, J.S.Joseph, M.J.Buchmeier, P.Kuhn, and K.Wüthrich (2009).
Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3.
  J Virol, 83, 12998-13008.
PDB code: 2k87
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.  
17787018 C.A.Chénard, and S.Richard (2008).
New implications for the QUAKING RNA binding protein in human disease.
  J Neurosci Res, 86, 233-242.  
18978773 D.D.Licatalosi, A.Mele, J.J.Fak, J.Ule, M.Kayikci, S.W.Chi, T.A.Clark, A.C.Schweitzer, J.E.Blume, X.Wang, J.C.Darnell, and R.B.Darnell (2008).
HITS-CLIP yields genome-wide insights into brain alternative RNA processing.
  Nature, 456, 464-469.  
18755838 E.Vanrobays, A.Leplus, Y.N.Osheim, A.L.Beyer, L.Wacheul, and D.L.Lafontaine (2008).
TOR regulates the subcellular distribution of DIM2, a KH domain protein required for cotranscriptional ribosome assembly and pre-40S ribosome export.
  RNA, 14, 2061-2073.  
18559344 I.Keren, L.Klipcan, A.Bezawork-Geleta, M.Kolton, F.Shaya, and O.Ostersetzer-Biran (2008).
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  J Biol Chem, 283, 23333-23342.  
18597886 K.E.Lukong, K.W.Chang, E.W.Khandjian, and S.Richard (2008).
RNA-binding proteins in human genetic disease.
  Trends Genet, 24, 416-425.  
18422648 R.Valverde, L.Edwards, and L.Regan (2008).
Structure and function of KH domains.
  FEBS J, 275, 2712-2726.  
18701464 Z.Du, S.Fenn, R.Tjhen, and T.L.James (2008).
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  J Biol Chem, 283, 28757-28766.  
17105995 A.Barkan, L.Klipcan, O.Ostersetzer, T.Kawamura, Y.Asakura, and K.P.Watkins (2007).
The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein.
  RNA, 13, 55-64.  
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.  
17569664 K.Januszyk, P.W.Li, V.Villareal, D.Branciforte, H.Wu, Y.Xie, J.Feigon, J.A.Loo, S.L.Martin, and R.T.Clubb (2007).
Identification and solution structure of a highly conserved C-terminal domain within ORF1p required for retrotransposition of long interspersed nuclear element-1.
  J Biol Chem, 282, 24893-24904.
PDB code: 2jrb
17437720 M.F.García-Mayoral, D.Hollingworth, L.Masino, I.Díaz-Moreno, G.Kelly, R.Gherzi, C.F.Chou, C.Y.Chen, and A.Ramos (2007).
The structure of the C-terminal KH domains of KSRP reveals a noncanonical motif important for mRNA degradation.
  Structure, 15, 485-498.
PDB codes: 2hh2 2hh3
17654551 M.Z.Jia, J.Ohtsuka, W.C.Lee, K.Nagata, and M.Tanokura (2007).
Crystal structure of Dim2p: a preribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 A.
  Proteins, 69, 428-432.
PDB code: 2e3u
17194772 P.Banerjee, S.Nayar, S.Hebbar, C.F.Fox, M.C.Jacobs, J.H.Park, J.J.Fernandes, and T.C.Dockendorff (2007).
Substitution of critical isoleucines in the KH domains of Drosophila fragile X protein results in partial loss-of-function phenotypes.
  Genetics, 175, 1241-1250.  
17426136 S.Fenn, Z.Du, J.K.Lee, R.Tjhen, R.M.Stroud, and T.L.James (2007).
Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution.
  Nucleic Acids Res, 35, 2651-2660.
PDB code: 2p2r
17972918 S.Hare, W.Fischer, R.Williams, L.Terradot, R.Bayliss, R.Haas, and G.Waksman (2007).
Identification, structure and mode of action of a new regulator of the Helicobacter pylori HP0525 ATPase.
  EMBO J, 26, 4926-4934.
PDB code: 2pt7
17526645 Z.Du, J.K.Lee, S.Fenn, R.Tjhen, R.M.Stroud, and T.L.James (2007).
X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2.
  RNA, 13, 1043-1051.
PDB codes: 2pqu 2py9
16738408 F.W.Scherrer, and M.Spingola (2006).
A subset of Mer1p-dependent introns requires Bud13p for splicing activation and nuclear retention.
  RNA, 12, 1361-1372.  
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.  
17065982 J.Ule, G.Stefani, A.Mele, M.Ruggiu, X.Wang, B.Taneri, T.Gaasterland, B.J.Blencowe, and R.B.Darnell (2006).
An RNA map predicting Nova-dependent splicing regulation.
  Nature, 444, 580-586.  
16428607 N.H.Chmiel, D.C.Rio, and J.A.Doudna (2006).
Distinct contributions of KH domains to substrate binding affinity of Drosophila P-element somatic inhibitor protein.
  RNA, 12, 283-291.  
17381312 R.B.Darnell (2006).
Developing global insight into RNA regulation.
  Cold Spring Harb Symp Quant Biol, 71, 321-327.  
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.  
16476777 T.P.Munro, S.Kwon, B.J.Schnapp, and D.St Johnston (2006).
A repeated IMP-binding motif controls oskar mRNA translation and anchoring independently of Drosophila melanogaster IMP.
  J Cell Biol, 172, 577-588.  
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
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
15933722 B.K.Dredge, G.Stefani, C.C.Engelhard, and R.B.Darnell (2005).
Nova autoregulation reveals dual functions in neuronal splicing.
  EMBO J, 24, 1608-1620.  
15861180 C.Bagni, and W.T.Greenough (2005).
From mRNP trafficking to spine dysmorphogenesis: the roots of fragile X syndrome.
  Nat Rev Neurosci, 6, 376-387.  
15670167 I.Pozdnyakova, and L.Regan (2005).
New insights into Fragile X syndrome. Relating genotype to phenotype at the molecular level.
  FEBS J, 272, 872-878.  
15805463 J.C.Darnell, C.E.Fraser, O.Mostovetsky, G.Stefani, T.A.Jones, S.R.Eddy, and R.B.Darnell (2005).
Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes.
  Genes Dev, 19, 903-918.  
16098133 J.C.Darnell, O.Mostovetsky, and R.B.Darnell (2005).
FMRP RNA targets: identification and validation.
  Genes Brain Behav, 4, 341-349.  
16041372 J.Ule, A.Ule, J.Spencer, A.Williams, J.S.Hu, M.Cline, H.Wang, T.Clark, C.Fraser, M.Ruggiu, B.R.Zeeberg, D.Kane, J.N.Weinstein, J.Blume, and R.B.Darnell (2005).
Nova regulates brain-specific splicing to shape the synapse.
  Nat Genet, 37, 844-852.  
15756586 M.Sidiqi, J.A.Wilce, C.J.Porter, A.Barker, P.J.Leedman, and M.C.Wilce (2005).
Formation of an alphaCP1-KH3 complex with UC-rich RNA.
  Eur Biophys J, 34, 423-429.  
15731341 M.Sidiqi, J.A.Wilce, J.P.Vivian, C.J.Porter, A.Barker, P.J.Leedman, and M.C.Wilce (2005).
Structure and RNA binding of the third KH domain of poly(C)-binding protein 1.
  Nucleic Acids Res, 33, 1213-1221.
PDB code: 1wvn
15643068 P.Becht, E.Vollmeister, and M.Feldbrügge (2005).
Role for RNA-binding proteins implicated in pathogenic development of Ustilago maydis.
  Eukaryot Cell, 4, 121-133.  
16077728 R.Singh, and J.Valcárcel (2005).
Building specificity with nonspecific RNA-binding proteins.
  Nat Struct Mol Biol, 12, 645-653.  
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
15853794 Y.Chen, and G.Varani (2005).
Protein families and RNA recognition.
  FEBS J, 272, 2088-2097.  
16186123 Z.Du, J.K.Lee, R.Tjhen, S.Li, H.Pan, R.M.Stroud, and T.L.James (2005).
Crystal structure of the first KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 A.
  J Biol Chem, 280, 38823-38830.
PDB code: 2axy
15170865 B.B.Yeap, J.A.Wilce, and P.J.Leedman (2004).
The androgen receptor mRNA.
  Bioessays, 26, 672-682.  
15063529 D.Hinkle, J.Glanzer, A.Sarabi, T.Pajunen, J.Zielinski, B.Belt, K.Miyashiro, T.McIntosh, and J.Eberwine (2004).
Single neurons as experimental systems in molecular biology.
  Prog Neurobiol, 72, 129-142.  
14994288 J.C.Darnell, S.T.Warren, and R.B.Darnell (2004).
The fragile X mental retardation protein, FMRP, recognizes G-quartets.
  Ment Retard Dev Disabil Res Rev, 10, 49-52.  
15048824 J.M.Hicks, and V.L.Hsu (2004).
The extended left-handed helix: a simple nucleic acid-binding motif.
  Proteins, 55, 330-338.  
15314207 J.Nielsen, M.A.Kristensen, M.Willemoës, F.C.Nielsen, and J.Christiansen (2004).
Sequential dimerization of human zipcode-binding protein IMP1 on RNA: a cooperative mechanism providing RNP stability.
  Nucleic Acids Res, 32, 4368-4376.  
15159542 K.B.Arnvig, S.Pennell, B.Gopal, and M.J.Colston (2004).
A high-affinity interaction between NusA and the rrn nut site in Mycobacterium tuberculosis.
  Proc Natl Acad Sci U S A, 101, 8325-8330.  
15367696 K.Musunuru, and R.B.Darnell (2004).
Determination and augmentation of RNA sequence specificity of the Nova K-homology domains.
  Nucleic Acids Res, 32, 4852-4861.  
15105376 M.H.Lee, and T.Schedl (2004).
Translation repression by GLD-1 protects its mRNA targets from nonsense-mediated mRNA decay in C. elegans.
  Genes Dev, 18, 1047-1059.  
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.  
14994290 R.Willemsen, B.A.Oostra, G.J.Bassell, and J.Dictenberg (2004).
The fragile X syndrome: from molecular genetics to neurobiology.
  Ment Retard Dev Disabil Res Rev, 10, 60-67.  
15310842 T.C.Mockler, X.Yu, D.Shalitin, D.Parikh, T.P.Michael, J.Liou, J.Huang, Z.Smith, J.M.Alonso, J.R.Ecker, J.Chory, and C.Lin (2004).
Regulation of flowering time in Arabidopsis by K homology domain proteins.
  Proc Natl Acad Sci U S A, 101, 12759-12764.  
14718656 T.Kasai, M.Inoue, S.Koshiba, T.Yabuki, M.Aoki, E.Nunokawa, E.Seki, T.Matsuda, N.Matsuda, Y.Tomo, M.Shirouzu, T.Terada, N.Obayashi, H.Hamana, N.Shinya, A.Tatsuguchi, S.Yasuda, M.Yoshida, H.Hirota, Y.Matsuo, K.Tani, H.Suzuki, T.Arakawa, P.Carninci, J.Kawai, Y.Hayashizaki, T.Kigawa, and S.Yokoyama (2004).
Solution structure of a BolA-like protein from Mus musculus.
  Protein Sci, 13, 545-548.
PDB code: 1v9j
15331611 Z.Du, J.Yu, Y.Chen, R.Andino, and T.L.James (2004).
Specific recognition of the C-rich strand of human telomeric DNA and the RNA template of human telomerase by the first KH domain of human poly(C)-binding protein-2.
  J Biol Chem, 279, 48126-48134.  
14612387 A.N.Chkheidze, and S.A.Liebhaber (2003).
A novel set of nuclear localization signals determine distributions of the alphaCP RNA-binding proteins.
  Mol Cell Biol, 23, 8405-8415.  
12592003 A.Ramos, D.Hollingworth, and A.Pastore (2003).
The role of a clinically important mutation in the fold and RNA-binding properties of KH motifs.
  RNA, 9, 293-298.  
12808107 B.K.Dredge, and R.B.Darnell (2003).
Nova regulates GABA(A) receptor gamma2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer.
  Mol Cell Biol, 23, 4687-4700.  
12600940 B.R.Szymczyna, J.Bowman, S.McCracken, A.Pineda-Lucena, Y.Lu, B.Cox, M.Lambermon, B.R.Graveley, C.H.Arrowsmith, and B.J.Blencowe (2003).
Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing.
  Genes Dev, 17, 461-475.
PDB code: 1mp1
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
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.  
14615540 J.Ule, K.B.Jensen, M.Ruggiu, A.Mele, A.Ule, and R.B.Darnell (2003).
CLIP identifies Nova-regulated RNA networks in the brain.
  Science, 302, 1212-1215.  
14643926 K.E.Lukong, and S.Richard (2003).
Sam68, the KH domain-containing superSTAR.
  Biochim Biophys Acta, 1653, 73-86.  
12507992 K.L.Farina, S.Huttelmaier, K.Musunuru, R.Darnell, and R.H.Singer (2003).
Two ZBP1 KH domains facilitate beta-actin mRNA localization, granule formation, and cytoskeletal attachment.
  J Cell Biol, 160, 77-87.  
12931193 R.Sugiura, A.Kita, Y.Shimizu, H.Shuntoh, S.O.Sio, and T.Kuno (2003).
Feedback regulation of MAPK signalling by an RNA-binding protein.
  Nature, 424, 961-965.  
12972621 S.A.Waggoner, and S.A.Liebhaber (2003).
Identification of mRNAs associated with alphaCP2-containing RNP complexes.
  Mol Cell Biol, 23, 7055-7067.  
12594214 Y.J.Sung, N.Dolzhanskaya, S.L.Nolin, T.Brown, J.R.Currie, and R.B.Denman (2003).
The fragile X mental retardation protein FMRP binds elongation factor 1A mRNA and negatively regulates its translation in vivo.
  J Biol Chem, 278, 15669-15678.  
12403469 A.Git, and N.Standart (2002).
The KH domains of Xenopus Vg1RBP mediate RNA binding and self-association.
  RNA, 8, 1319-1333.  
11914064 A.Ramos, D.Hollingworth, S.A.Major, S.Adinolfi, G.Kelly, F.W.Muskett, and A.Pastore (2002).
Role of dimerization in KH/RNA complexes: the example of Nova KH3.
  Biochemistry, 41, 4193-4201.  
12093748 D.T.Braddock, J.L.Baber, D.Levens, and G.M.Clore (2002).
Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA.
  EMBO J, 21, 3476-3485.
PDB code: 1j5k
12429100 G.J.Ostheimer, A.Barkan, and B.W.Matthews (2002).
Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins.
  Structure, 10, 1593-1601.
PDB code: 1ln4
11753425 J.P.Staley (2002).
Hanging on to the branch.
  Nat Struct Biol, 9, 5-7.  
12177293 N.B.Leontis, J.Stombaugh, and E.Westhof (2002).
The non-Watson-Crick base pairs and their associated isostericity matrices.
  Nucleic Acids Res, 30, 3497-3531.  
12052912 W.T.O'Donnell, and S.T.Warren (2002).
A decade of molecular studies of fragile X syndrome.
  Annu Rev Neurosci, 25, 315-338.  
11481485 A.Beletskii, Y.K.Hong, J.Pehrson, M.Egholm, and W.M.Strauss (2001).
PNA interference mapping demonstrates functional domains in the noncoding RNA Xist.
  Proc Natl Acad Sci U S A, 98, 9215-9220.  
11565747 A.K.Amarasinghe, R.MacDiarmid, M.D.Adams, and D.C.Rio (2001).
An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element.
  RNA, 7, 1239-1253.  
11253358 B.K.Dredge, A.D.Polydorides, and R.B.Darnell (2001).
The splice of life: alternative splicing and neurological disease.
  Nat Rev Neurosci, 2, 43-50.  
11565746 B.Till, C.Schmitz-Linneweber, R.Williams-Carrier, and A.Barkan (2001).
CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin.
  RNA, 7, 1227-1238.  
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.  
11719189 J.C.Darnell, K.B.Jensen, P.Jin, V.Brown, S.T.Warren, and R.B.Darnell (2001).
Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function.
  Cell, 107, 489-499.  
11179892 J.M.Pérez-Cañadillas, and G.Varani (2001).
Recent advances in RNA-protein recognition.
  Curr Opin Struct Biol, 11, 53-58.  
11283311 K.Musunuru, and R.B.Darnell (2001).
Paraneoplastic neurologic disease antigens: RNA-binding proteins and signaling proteins in neuronal degeneration.
  Annu Rev Neurosci, 24, 239-262.  
11562350 M.H.Lee, and T.Schedl (2001).
Identification of in vivo mRNA targets of GLD-1, a maxi-KH motif containing protein required for C. elegans germ cell development.
  Genes Dev, 15, 2408-2420.  
11160884 N.V.Grishin (2001).
KH domain: one motif, two folds.
  Nucleic Acids Res, 29, 638-643.  
11340052 S.L.Cohen, and B.T.Chait (2001).
Mass spectrometry as a tool for protein crystallography.
  Annu Rev Biophys Biomol Struct, 30, 67-85.  
11359897 T.Imai, A.Tokunaga, T.Yoshida, M.Hashimoto, K.Mikoshiba, G.Weinmaster, M.Nakafuku, and H.Okano (2001).
The neural RNA-binding protein Musashi1 translationally regulates mammalian numb gene expression by interacting with its mRNA.
  Mol Cell Biol, 21, 3888-3900.  
11517327 Y.Zhu, C.Qi, W.Q.Cao, A.V.Yeldandi, M.S.Rao, and J.K.Reddy (2001).
Cloning and characterization of PIMT, a protein with a methyltransferase domain, which interacts with and enhances nuclear receptor coactivator PRIP function.
  Proc Natl Acad Sci U S A, 98, 10380-10385.  
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
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
10829067 A.D.Polydorides, H.J.Okano, Y.Y.Yang, G.Stefani, and R.B.Darnell (2000).
A brain-enriched polypyrimidine tract-binding protein antagonizes the ability of Nova to regulate neuron-specific alternative splicing.
  Proc Natl Acad Sci U S A, 97, 6350-6355.  
10775271 B.Rutz, and B.Séraphin (2000).
A dual role for BBP/ScSF1 in nuclear pre-mRNA retention and splicing.
  EMBO J, 19, 1873-1886.  
10821674 J.L.Baber, D.Levens, D.Libutti, and N.Tjandra (2000).
Chemical shift mapped DNA-binding sites and 15N relaxation analysis of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K.
  Biochemistry, 39, 6022-6032.  
10719891 K.B.Jensen, B.K.Dredge, G.Stefani, R.Zhong, R.J.Buckanovich, H.J.Okano, Y.Y.Yang, and R.B.Darnell (2000).
Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability.
  Neuron, 25, 359-371.  
10811881 K.B.Jensen, K.Musunuru, H.A.Lewis, S.K.Burley, and R.B.Darnell (2000).
The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain.
  Proc Natl Acad Sci U S A, 97, 5740-5745.  
11080643 M.F.Symmons, G.H.Jones, and B.F.Luisi (2000).
A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation.
  Structure, 8, 1215-1226.
PDB codes: 1e3h 1e3p
10983980 M.Spingola, and M.Ares (2000).
A yeast intronic splicing enhancer and Nam8p are required for Mer1p-activated splicing.
  Mol Cell, 6, 329-338.  
10896472 P.B.Rupert, and A.R.Ferré-D'amaré (2000).
SRPrises in RNA-protein recognition.
  Structure, 8, R99-104.  
10719879 P.J.Grabowski (2000).
Genetic evidence for a Nova regulator of alternative splicing in the brain.
  Neuron, 25, 254-256.  
10906214 T.M.Soliman, and S.J.Silverstein (2000).
Identification of an export control sequence and a requirement for the KH domains in ICP27 from herpes simplex virus type 1.
  J Virol, 74, 7600-7609.  
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.  
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 code is shown on the right.

 

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