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PDBsum entry 2f8k

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protein dna_rna links
RNA binding protein/ RNA PDB id
2f8k
Jmol
Contents
Protein chain
84 a.a. *
DNA/RNA
Waters ×117
* Residue conservation analysis
PDB id:
2f8k
Name: RNA binding protein/ RNA
Title: Sequence specific recognition of RNA hairpins by the sam dom vts1
Structure: 5'-r( Up Ap Ap Up Cp Up Up Up Gp Ap Cp Ap Gp Ap U chain: b. Engineered: yes. Other_details: sre23. Protein vts1. Chain: a. Synonym: vti1-2 suppressor protein 1. Engineered: yes
Source: Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: vts1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.230     R-free:   0.277
Authors: T.Aviv,Z.Lin,G.Ben-Ari,C.A.Smibert,F.Sicheri
Key ref:
T.Aviv et al. (2006). Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat Struct Mol Biol, 13, 168-176. PubMed id: 16429151 DOI: 10.1038/nsmb1053
Date:
02-Dec-05     Release date:   24-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q08831  (VTS1_YEAST) -  Protein VTS1
Seq:
Struc:
 
Seq:
Struc:
523 a.a.
84 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1038/nsmb1053 Nat Struct Mol Biol 13:168-176 (2006)
PubMed id: 16429151  
 
 
Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p.
T.Aviv, Z.Lin, G.Ben-Ari, C.A.Smibert, F.Sicheri.
 
  ABSTRACT  
 
The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that function as sequence-specific RNA-binding domains. Here we report the 2.0-A X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand. Specificity of RNA binding arises from the association of a guanosine loop base with a shallow pocket on the SAM domain and from multiple SAM domain contacts to the unique backbone structure of the loop, defined in part by a nonplanar base pair within the loop. We have validated NNF1 as an endogenous target of Vts1p among 79 transcripts that copurify with Vts1p. Bioinformatic analysis of these mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably more stringent than that of the isolated SAM domain in vitro.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The SRE pentaloop structure exhibits similarity to the UNCG and SECIS loops. (a) Stereo diagram of the SRE pentaloop. Dashed lines indicate hydrogen bonds. (b,c) Stereo diagrams of the SRE crystal structure overlaid with the UNCG (b, green; PDB entry 1F7Y; ref. 21) and SECIS (c, blue; PDB entry 1WSU; ref. 22) RNA loops, respectively. Superpositions were generated with Swiss-PDB viewer (http://www.expasy.org/spdbv/).
Figure 3.
Figure 3. Features of the Vts1p-SAM–RNA binding interface. (a) Schematic diagram of SRE recognition by Vts1p-SAM. Black dashed lines, hydrogen bonds; green dashed lines, hydrophobic interactions; blue background, the stem of the SRE; pink background, the pentaloop; red circles, phosphate groups; blue ovals, bridging water molecules. The labeled protein residues are colored according to their originating secondary structure elements as shown in the upper left schematic. (b) Stereo diagram of the Vts1p-SAM–SRE binding interface centered on SRE loop position G3. Red spheres, water molecules participating in bridging interactions between protein and RNA; dashed lines, hydrogen bonds involving the G3 base.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 168-176) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20959291 D.P.Riordan, D.Herschlag, and P.O.Brown (2011).
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.
  Nucleic Acids Res, 39, 1501-1509.  
21081899 M.Jeske, B.Moritz, A.Anders, and E.Wahle (2011).
Smaug assembles an ATP-dependent stable complex repressing nanos mRNA translation at multiple levels.
  EMBO J, 30, 90.  
20007605 C.H.Lee, Y.K.Shin, T.T.Phung, J.S.Bae, Y.H.Kang, T.A.Nguyen, J.H.Kim, D.H.Kim, M.J.Kang, S.H.Bae, and Y.S.Seo (2010).
Involvement of Vts1, a structure-specific RNA-binding protein, in Okazaki fragment processing in yeast.
  Nucleic Acids Res, 38, 1583-1595.  
20617199 H.Kazan, D.Ray, E.T.Chan, T.R.Hughes, and Q.Morris (2010).
RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins.
  PLoS Comput Biol, 6, e1000832.  
20108951 J.D.Ballin, J.P.Prevas, C.R.Ross, E.A.Toth, G.M.Wilson, and M.T.Record (2010).
Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH.
  Biochemistry, 49, 2018-2030.  
20418358 X.Li, G.Quon, H.D.Lipshitz, and Q.Morris (2010).
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure.
  RNA, 16, 1096-1107.  
19401680 B.C.Foat, and G.D.Stormo (2009).
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs.
  Mol Syst Biol, 5, 268.  
19561594 D.Ray, H.Kazan, E.T.Chan, L.P.Castillo, S.Chaudhry, S.Talukder, B.J.Blencowe, Q.Morris, and T.R.Hughes (2009).
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.
  Nat Biotechnol, 27, 667-670.  
18255277 A.Serganov, and D.J.Patel (2008).
Towards deciphering the principles underlying an mRNA recognition code.
  Curr Opin Struct Biol, 18, 120-129.  
18959479 D.J.Hogan, D.P.Riordan, A.P.Gerber, D.Herschlag, and P.O.Brown (2008).
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.
  PLoS Biol, 6, e255.  
18794360 J.L.Semotok, H.Luo, R.L.Cooperstock, A.Karaiskakis, H.K.Vari, C.A.Smibert, and H.D.Lipshitz (2008).
Drosophila maternal Hsp83 mRNA destabilization is directed by multiple SMAUG recognition elements in the open reading frame.
  Mol Cell Biol, 28, 6757-6772.  
18469165 L.M.Rendl, M.A.Bieman, and C.A.Smibert (2008).
S. cerevisiae Vts1p induces deadenylation-dependent transcript degradation and interacts with the Ccr4p-Pop2p-Not deadenylase complex.
  RNA, 14, 1328-1336.  
18263618 M.Schwalbe, O.Ohlenschläger, A.Marchanka, R.Ramachandran, S.Häfner, T.Heise, and M.Görlach (2008).
Solution structure of stem-loop alpha of the hepatitis B virus post-transcriptional regulatory element.
  Nucleic Acids Res, 36, 1681-1689.
PDB code: 2jym
18353859 R.P.Bahadur, M.Zacharias, and J.Janin (2008).
Dissecting protein-RNA recognition sites.
  Nucleic Acids Res, 36, 2705-2716.  
18287031 T.Rajakulendran, M.Sahmi, I.Kurinov, M.Tyers, M.Therrien, and F.Sicheri (2008).
CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling.
  Proc Natl Acad Sci U S A, 105, 2836-2841.
PDB codes: 3bs5 3bs7
18546154 W.Liao, Z.Bao, C.Cheng, Y.K.Mok, and W.S.Wong (2008).
Dendritic cell-derived interferon-gamma-induced protein mediates tumor necrosis factor-alpha stimulation of human lung fibroblasts.
  Proteomics, 8, 2640-2650.  
17509066 J.L.Semotok, and H.D.Lipshitz (2007).
Regulation and function of maternal mRNA destabilization during early Drosophila development.
  Differentiation, 75, 482-506.  
17724133 Y.Kim, P.Zhou, L.Qian, J.Z.Chuang, J.Lee, C.Li, C.Iadecola, C.Nathan, and A.Ding (2007).
MyD88-5 links mitochondria, microtubules, and JNK3 in neurons and regulates neuronal survival.
  J Exp Med, 204, 2063-2074.  
16793273 E.D.Gundelfinger, T.M.Boeckers, M.K.Baron, and J.U.Bowie (2006).
A role for zinc in postsynaptic density asSAMbly and plasticity?
  Trends Biochem Sci, 31, 366-373.  
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.