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PDBsum entry 1s03
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protein dna_rna metals links
Transcription/RNA PDB id
1s03

 

 

 

 

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Contents
Protein chains
127 a.a. *
DNA/RNA
Metals
_ZN ×17
Waters ×5
* Residue conservation analysis
PDB id:
1s03
Name: Transcription/RNA
Title: The structure of a ribosomal protein s8/spc operon mRNA complex
Structure: 47-mer. Chain: a, b. Engineered: yes. 30s ribosomal protein s8. Chain: h, g
Source: Synthetic: yes. Other_details: RNA was prepared by in vitro transciption, sequence from e. Coli spc operon. Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.70Å     R-factor:   0.237     R-free:   0.273
Authors: H.J.Merianos,J.Wang,P.B.Moore
Key ref: H.J.Merianos et al. (2004). The structure of a ribosomal protein S8/spc operon mRNA complex. Rna, 10, 954-964. PubMed id: 15146079
Date:
29-Dec-03     Release date:   25-May-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A7W7  (RS8_ECOLI) -  Small ribosomal subunit protein uS8 from Escherichia coli (strain K12)
Seq:
Struc: 		130 a.a.
127 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  G-G-A-C-G-A-U-G-G-C-G-A-A-A-C-U-G-C-A-U-G-A-G-G-C-A-A-U-U-C-A-U-G-C-A-A-G-U-C- 47 bases
  G-G-A-C-G-A-U-G-G-C-G-A-A-A-C-U-G-C-A-U-G-A-G-G-C-A-A-U-U-C-A-U-G-C-A-A-G-U-C- 47 bases

 

 
Rna 10:954-964 (2004)
PubMed id: 15146079  
 
 
The structure of a ribosomal protein S8/spc operon mRNA complex.
H.J.Merianos, J.Wang, P.B.Moore.
 
  ABSTRACT  
 
In bacteria, translation of all the ribosomal protein cistrons in the spc operon mRNA is repressed by the binding of the product of one of them, S8, to an internal sequence at the 5' end of the L5 cistron. The way in which the first two genes of the spc operon are regulated, retroregulation, is mechanistically distinct from translational repression by S8 of the genes from L5 onward. A 2.8 A resolution crystal structure has been obtained of Escherichia coli S8 bound to this site. Despite sequence differences, the structure of this complex is almost identical to that of the S8/helix 21 complex seen in the small ribosomal subunit, consistent with the hypothesis that autogenous regulation of ribosomal protein synthesis results from conformational similarities between mRNAs and rRNAs. S8 binding must repress the translation of its own mRNA by inhibiting the formation of a ribosomal initiation complex at the start of the L5 cistron.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21320180 T.Siibak, L.Peil, A.Dönhöfer, A.Tats, M.Remm, D.N.Wilson, T.Tenson, and J.Remme (2011).
Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins.
  Mol Microbiol, 80, 54-67.  
19377483 M.C.Hammond, A.Wachter, and R.R.Breaker (2009).
A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs.
  Nat Struct Mol Biol, 16, 541-549.  
19531245 M.M.Meyer, T.D.Ames, D.P.Smith, Z.Weinberg, M.S.Schwalbach, S.J.Giovannoni, and R.R.Breaker (2009).
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'.
  BMC Genomics, 10, 268.  
19385727 P.Babitzke, C.S.Baker, and T.Romeo (2009).
Regulation of translation initiation by RNA binding proteins.
  Annu Rev Microbiol, 63, 27-44.  
18204466 S.D.Gilbert, R.P.Rambo, D.Van Tyne, and R.T.Batey (2008).
Structure of the SAM-II riboswitch bound to S-adenosylmethionine.
  Nat Struct Mol Biol, 15, 177-182.
PDB code: 2qwy
17439971 F.Allemand, J.Haentjens, C.Chiaruttini, C.Royer, and M.Springer (2007).
Escherichia coli ribosomal protein L20 binds as a single monomer to its own mRNA bearing two potential binding sites.
  Nucleic Acids Res, 35, 3016-3031.  
17289755 N.Choonee, S.Even, L.Zig, and H.Putzer (2007).
Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism.
  Nucleic Acids Res, 35, 1578-1588.  
17889647 S.Marzi, A.G.Myasnikov, A.Serganov, C.Ehresmann, P.Romby, M.Yusupov, and B.P.Klaholz (2007).
Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.
  Cell, 130, 1019-1031.
PDB code: 2vaz
16707260 R.T.Batey (2006).
Structures of regulatory elements in mRNAs.
  Curr Opin Struct Biol, 16, 299-306.  
17139090 S.Tishchenko, E.Nikonova, A.Nikulin, N.Nevskaya, S.Volchkov, W.Piendl, M.Garber, and S.Nikonov (2006).
Structure of the ribosomal protein L1-mRNA complex at 2.1 A resolution: common features of crystal packing of L1-RNA complexes.
  Acta Crystallogr D Biol Crystallogr, 62, 1545-1554.
PDB code: 2hw8
15659579 N.Nevskaya, S.Tishchenko, A.Gabdoulkhakov, E.Nikonova, O.Nikonov, A.Nikulin, O.Platonova, M.Garber, S.Nikonov, and W.Piendl (2005).
Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA.
  Nucleic Acids Res, 33, 478-485.
PDB code: 1u63
15750802 W.C.Winkler (2005).
Metabolic monitoring by bacterial mRNAs.
  Arch Microbiol, 183, 151-159.  
16153177 W.C.Winkler, and R.R.Breaker (2005).
Regulation of bacterial gene expression by riboswitches.
  Annu Rev Microbiol, 59, 487-517.  
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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