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PDBsum entry 1p27

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protein Protein-protein interface(s) links
RNA binding protein PDB id
1p27
Jmol
Contents
Protein chains
144 a.a. *
92 a.a. *
Waters ×100
* Residue conservation analysis
PDB id:
1p27
Name: RNA binding protein
Title: Crystal structure of the human y14/magoh complex
Structure: Mago nashi protein homolog. Chain: a, c. Engineered: yes. RNA-binding protein 8a. Chain: b, d. Synonym: RNA binding motif protein 8a, ribonucleoprotein rb binding protein y14, binder of ovca1- 1, bov-1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: magoh. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rbm8a or rbm8.
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.222     R-free:   0.268
Authors: C.K.Lau,M.D.Diem,G.Dreyfuss,G.D.Van Duyne
Key ref:
C.K.Lau et al. (2003). Structure of the Y14-Magoh core of the exon junction complex. Curr Biol, 13, 933-941. PubMed id: 12781131 DOI: 10.1016/S0960-9822(03)00328-2
Date:
14-Apr-03     Release date:   19-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61326  (MGN_HUMAN) -  Protein mago nashi homolog
Seq:
Struc:
146 a.a.
144 a.a.
Protein chains
Pfam   ArchSchema ?
Q9Y5S9  (RBM8A_HUMAN) -  RNA-binding protein 8A
Seq:
Struc:
174 a.a.
92 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     catalytic step 2 spliceosome   8 terms 
  Biological process     transport   16 terms 
  Biochemical function     protein binding     5 terms  

 

 
DOI no: 10.1016/S0960-9822(03)00328-2 Curr Biol 13:933-941 (2003)
PubMed id: 12781131  
 
 
Structure of the Y14-Magoh core of the exon junction complex.
C.K.Lau, M.D.Diem, G.Dreyfuss, G.D.Van Duyne.
 
  ABSTRACT  
 
BACKGROUND: Splicing of pre-mRNA in eukaryotes imprints the resulting mRNA with a specific multiprotein complex, the exon-exon junction complex (EJC), at the sites of intron removal. The proteins of the EJC, Y14, Magoh, Aly/REF, RNPS1, Srm160, and Upf3, play critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. Y14 and Magoh are of particular interest because they remain associated with the mRNA in the same position after its export to the cytoplasm and require translation of the mRNA for removal. This tenacious, persistent, splicing-dependent, yet RNA sequence-independent, association suggests an important signaling function and must require distinct structural features for these proteins. RESULTS: We describe the high-resolution structure and biochemical properties of the highly conserved human Y14 and Magoh proteins. Magoh has an unusual structure comprised of an extremely flat, six-stranded anti-parallel beta sheet packed against two helices. Surprisingly, Magoh binds with high affinity to the RNP motif RNA binding domain (RBD) of Y14 and completely masks its RNA binding surface. CONCLUSIONS: The structure and properties of the Y14-Magoh complex suggest how the pre-mRNA splicing machinery might control the formation of a stable EJC-mRNA complex at splice junctions.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structure of Human Magoh(A) Alignment of a diverse subset of known Magoh sequences. The shaded regions indicate ≥80% sequence identity. Secondary structure assignments are shown above the alignments, and residues contacting Y14 (< 3.8 Å) are marked with an asterisk. Hs, human; Dm, D. melanogaster; Ce, C. elegans; At, A. thaliana; Sp, S. pombe.(B) A ribbon diagram of Magoh as seen bound to Y14.(C) σ[A]-weighted 2Fo-Fc electron density for the refined structure at 2 Å resolution, contoured at 1.4 σ. The orientation of the indicated β strands is the same as that shown in (B).The molecular drawings in Figure 2, Figure 3, Figure 4, Figure 5 and Figure 6 were prepared with PYMOL [46].
Figure 3.
Figure 3. Sequence Conservation Mapped onto the Magoh StructureLight-blue residues correspond to the shaded regions in Figure 2A (≥80% identity), and dark-blue residues are less conserved.(A) Same orientation as in Figures 2B and 2C.(B) View from the opposite face, showing the concave surface formed by the β sheet extension.
 
  The above figures are reprinted by permission from Cell Press: Curr Biol (2003, 13, 933-941) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21268085 S.Park, and M.Jang (2011).
Phosphoproteome profiling for cold temperature perception.
  J Cell Biochem, 112, 633-642.  
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
19478851 N.H.Gehring, S.Lamprinaki, M.W.Hentze, and A.E.Kulozik (2009).
The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay.
  PLoS Biol, 7, e1000120.  
19589129 S.H.Ling, Z.Cheng, and H.Song (2009).
Structural aspects of RNA helicases in eukaryotic mRNA decay.
  Biosci Rep, 29, 339-349.  
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
18164611 H.Le Hir, and G.R.Andersen (2008).
Structural insights into the exon junction complex.
  Curr Opin Struct Biol, 18, 112-119.  
18559344 I.Keren, L.Klipcan, A.Bezawork-Geleta, M.Kolton, F.Shaya, and O.Ostersetzer-Biran (2008).
Characterization of the Molecular Basis of Group II Intron RNA Recognition by CRS1-CRM Domains.
  J Biol Chem, 283, 23333-23342.  
18982294 M.Kvaratskhelia, and S.F.Grice (2008).
Structural analysis of protein-RNA interactions with mass spectrometry.
  Methods Mol Biol, 488, 213-219.  
17668007 A.M.Tintaru, G.M.Hautbergue, A.M.Hounslow, M.L.Hung, L.Y.Lian, C.J.Craven, and S.A.Wilson (2007).
Structural and functional analysis of RNA and TAP binding to SF2/ASF.
  EMBO Rep, 8, 756-762.
PDB code: 2o3d
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.  
17375189 C.G.Noble, and H.Song (2007).
MLN51 stimulates the RNA-helicase activity of eIF4AIII.
  PLoS ONE, 2, e303.  
17095540 C.Merz, H.Urlaub, C.L.Will, and R.Lührmann (2007).
Protein composition of human mRNPs spliced in vitro and differential requirements for mRNP protein recruitment.
  RNA, 13, 116-128.  
17628520 D.H.Parma, P.E.Bennett, and R.E.Boswell (2007).
Mago Nashi and Tsunagi/Y14, respectively, regulate Drosophila germline stem cell differentiation and oocyte specification.
  Dev Biol, 308, 507-519.  
16953428 N.I.Park, and D.G.Muench (2007).
Biochemical and cellular characterization of the plant ortholog of PYM, a protein that interacts with the exon junction complex core proteins Mago and Y14.
  Planta, 225, 625-639.  
17352659 Y.F.Chang, J.S.Imam, and M.F.Wilkinson (2007).
The nonsense-mediated decay RNA surveillance pathway.
  Annu Rev Biochem, 76, 51-74.  
17077274 A.L.Silva, F.J.Pereira, A.Morgado, J.Kong, R.Martins, P.Faustino, S.A.Liebhaber, and L.Romão (2006).
The canonical UPF1-dependent nonsense-mediated mRNA decay is inhibited in transcripts carrying a short open reading frame independent of sequence context.
  RNA, 12, 2160-2170.  
16931718 C.B.Andersen, L.Ballut, J.S.Johansen, H.Chamieh, K.H.Nielsen, C.L.Oliveira, J.S.Pedersen, B.Séraphin, H.Le Hir, and G.R.Andersen (2006).
Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA.
  Science, 313, 1968-1972.
PDB codes: 2hxy 2hyi
16923391 F.Bono, J.Ebert, E.Lorentzen, and E.Conti (2006).
The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA.
  Cell, 126, 713-725.
PDB codes: 2j0q 2j0s 2j0u
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.  
16100109 I.a.W.Hsu, M.Hsu, C.Li, T.W.Chuang, R.I.Lin, and W.Y.Tarn (2005).
Phosphorylation of Y14 modulates its interaction with proteins involved in mRNA metabolism and influences its methylation.
  J Biol Chem, 280, 34507-34512.  
16170325 L.Ballut, B.Marchadier, A.Baguet, C.Tomasetto, B.Séraphin, and H.Le Hir (2005).
The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity.
  Nat Struct Mol Biol, 12, 861-869.  
15514923 L.C.Sutherland, N.D.Rintala-Maki, R.D.White, and C.D.Morin (2005).
RNA binding motif (RBM) proteins: a novel family of apoptosis modulators?
  J Cell Biochem, 94, 5.  
16209946 N.H.Gehring, J.B.Kunz, G.Neu-Yilik, S.Breit, M.H.Viegas, M.W.Hentze, and A.E.Kulozik (2005).
Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements.
  Mol Cell, 20, 65-75.  
16077728 R.Singh, and J.Valcárcel (2005).
Building specificity with nonspecific RNA-binding proteins.
  Nat Struct Mol Biol, 12, 645-653.  
16314458 T...Tange, T.Shibuya, M.S.Jurica, and M.J.Moore (2005).
Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core.
  RNA, 11, 1869-1883.  
15680326 Y.K.Kim, L.Furic, L.Desgroseillers, and L.E.Maquat (2005).
Mammalian Staufen1 recruits Upf1 to specific mRNA 3'UTRs so as to elicit mRNA decay.
  Cell, 120, 195-208.  
15215336 C.G.Noble, P.A.Walker, L.J.Calder, and I.A.Taylor (2004).
Rna14-Rna15 assembly mediates the RNA-binding capability of Saccharomyces cerevisiae cleavage factor IA.
  Nucleic Acids Res, 32, 3364-3375.  
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.  
14968132 F.Bono, J.Ebert, L.Unterholzner, T.Güttler, E.Izaurralde, and E.Conti (2004).
Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex.
  EMBO Rep, 5, 304-310.
PDB code: 1rk8
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
15048104 J.Lykke-Andersen (2004).
Making structural sense of nonsense-mediated decay.
  Nat Struct Mol Biol, 11, 305-306.  
15040442 L.E.Maquat (2004).
Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics.
  Nat Rev Mol Cell Biol, 5, 89-99.  
15342650 L.Jeffery, and S.Nakielny (2004).
Components of the DNA methylation system of chromatin control are RNA-binding proteins.
  J Biol Chem, 279, 49479-49487.  
15037772 N.Custódio, C.Carvalho, I.Condado, M.Antoniou, B.J.Blencowe, and M.Carmo-Fonseca (2004).
In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei.
  RNA, 10, 622-633.  
15034551 T.Shibuya, T...Tange, N.Sonenberg, and M.J.Moore (2004).
eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay.
  Nat Struct Mol Biol, 11, 346-351.  
15145352 T...Tange, A.Nott, and M.J.Moore (2004).
The ever-increasing complexities of the exon junction complex.
  Curr Opin Cell Biol, 16, 279-284.  
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.  
12942139 T.M.Hall (2003).
SAM breaks its stereotype.
  Nat Struct Biol, 10, 677-679.  
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.