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PDBsum entry 2b6g

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protein dna_rna links
RNA binding protein PDB id
2b6g
Jmol
Contents
Protein chain
81 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
2b6g
Name: RNA binding protein
Title: RNA recognition by the vts1 sam domain
Structure: 5'- r( Gp Gp Ap Gp Gp Cp Up Cp Up Gp Gp Cp Ap Gp Cp Up Up Up C) -3'. Chain: b. Fragment: smaug recognition element. Engineered: yes. Vts1p. Chain: a. Fragment: sam domain.
Source: Synthetic: yes. Other_details: RNA was produced by t7 polymerase based in vitro transcription. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: vts1p. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 1 models
Authors: L.W.Donaldson,P.E.Johnson
Key ref:
P.E.Johnson and L.W.Donaldson (2006). RNA recognition by the Vts1p SAM domain. Nat Struct Mol Biol, 13, 177-178. PubMed id: 16429155 DOI: 10.1038/nsmb1039
Date:
01-Oct-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.
81 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1038/nsmb1039 Nat Struct Mol Biol 13:177-178 (2006)
PubMed id: 16429155  
 
 
RNA recognition by the Vts1p SAM domain.
P.E.Johnson, L.W.Donaldson.
 
  ABSTRACT  
 
The putative yeast post-transcriptional regulator Vts1p and its related protein Smaug, from Drosophila melanogaster, each use a sterile alpha motif (SAM) domain to bind an RNA hairpin termed the Smaug recognition element (SRE). Here, we present the NMR structures of the Vts1p-SRE complex and the free SRE. Structural highlights include the direct recognition of a guanine base and the formation or stabilization of a base pair in the SRE loop.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Vts1p-SRE complex. (a) Three secondary structural elements (olive) augment the hydrophobic core of the Vts1p SAM domain (orange). The high-affinity RNA interaction draws upon base-specific contacts to G10 and sugar contacts to C8, U9 and G10. (b,c) The SRE-binding site of Vts1p.
Figure 2.
Figure 2. Structural changes in the SRE RNA upon protein binding. (a) Successive titration of Vts1p SAM domain reveals two new imino resonances in the bound molecule's spectrum. (b) Secondary structure of the SRE. (c,d) The SRE RNA in the Vts1p-SRE complex (c) and the free SRE (d).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 177-178) copyright 2006.  

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.  
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.  
18618697 A.Bhunia, P.N.Domadia, H.Mohanram, and S.Bhattacharjya (2009).
NMR structural studies of the Ste11 SAM domain in the dodecyl phosphocholine micelle.
  Proteins, 74, 328-343.  
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.  
19329536 T.J.Tavares, A.V.Beribisky, and P.E.Johnson (2009).
Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin.
  RNA, 15, 911-922.
PDB code: 2rpt
18255277 A.Serganov, and D.J.Patel (2008).
Towards deciphering the principles underlying an mRNA recognition code.
  Curr Opin Struct Biol, 18, 120-129.  
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
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
17901155 A.V.Beribisky, T.J.Tavares, A.N.Amborski, M.Motamed, A.E.Johnson, T.L.Mark, and P.E.Johnson (2007).
The three-dimensional structure of the Moorella thermoacetica selenocysteine insertion sequence RNA hairpin and its interaction with the elongation factor SelB.
  RNA, 13, 1948-1956.
PDB code: 2rlu
17519008 J.J.Kwan, and L.W.Donaldson (2007).
The NMR structure of the murine DLC2 SAM domain reveals a variant fold that is similar to a four-helix bundle.
  BMC Struct Biol, 7, 34.  
17509066 J.L.Semotok, and H.D.Lipshitz (2007).
Regulation and function of maternal mRNA destabilization during early Drosophila development.
  Differentiation, 75, 482-506.  
17600833 T.Ju, M.J.Ragusa, J.Hudak, A.C.Nairn, and W.Peti (2007).
Structural characterization of the neurabin sterile alpha motif domain.
  Proteins, 69, 192-198.
PDB code: 2gle
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.