PDBsum entry 1c06

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protein links
Ribosome PDB id
Protein chain
159 a.a. *
* Residue conservation analysis
PDB id:
Name: Ribosome
Title: Solution structure of ribosomal protein s4 delta 41, refined with dipolar couplings (ensemble of 16 structures)
Structure: Ribosomal protein s4 delta 41. Chain: a. Fragment: s4 delta 41 (s4 residues 42-200). Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 16 models
Authors: M.A.Markus,R.B.Gerstner,D.E.Draper,D.A.Torchia
Key ref:
M.A.Markus et al. (1999). Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases. J Mol Biol, 292, 375-387. PubMed id: 10493882 DOI: 10.1006/jmbi.1999.3061
14-Jul-99     Release date:   29-Sep-99    
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Protein chain
Pfam   ArchSchema ?
P81288  (RS4_GEOSE) -  30S ribosomal protein S4
200 a.a.
159 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     3 terms  


DOI no: 10.1006/jmbi.1999.3061 J Mol Biol 292:375-387 (1999)
PubMed id: 10493882  
Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases.
M.A.Markus, R.B.Gerstner, D.E.Draper, D.A.Torchia.
Prokaryotic protein S4 initiates assembly of the small ribosomal subunit by binding to 16 S rRNA. Residues 43-200 of S4 from Bacillus stearothermophilus (S4 Delta41) bind to both 16 S rRNA and to a mRNA pseudoknot. In order to obtain structure-based insights regarding RNA binding, we previously determined the solution structure of S4 Delta41 using NOE, hydrogen bond, and torsion angle restraints. S4 Delta41 is elongated, with two distinct subdomains, one all helical, the other including a beta-sheet. In contrast to the high resolution structures obtained for each individual subdomain, their relative orientation was not precisely defined because only 17 intersubdomain NOE restraints were determined. Compared to the 1.7 A crystal structure, when the sheet-containing subdomains are superimposed, the helical subdomain is twisted by almost 45 degrees about the long axis of the molecule in the solution structure. Because variations in subdomain orientation may explain how the protein recognizes multiple RNA targets, our current goal is to determine the orientation of the subdomains in solution with high precision. To this end, NOE assignments were re-examined. NOESY experiments on a specifically labeled sample revealed that one of the intersubdomain restraints had been misassigned. However, the revised set of NOE restraints produces solution structures that still have imprecisely defined subdomain orientations and that lie between the original NMR structure and the crystal structure. In contrast, augmenting the NOE restraints with N-H dipolar couplings, measured in uniaxial liquid crystalline phases, clearly establishes the relative orientation of the subdomains. Data obtained from two independent liquid crystalline milieux, DMPC/DHPC bicelles and the filamentous bacteriophage Pf1, show that the relative orientation of the subdomains in solution is quite similar to the subdomain orientation in the crystal structure. The solution structure, refined with dipolar data, is presented and its implications for S4's RNA binding activity are discussed.
  Selected figure(s)  
Figure 1.
Figure 1. Ribbon diagrams for (a) a representative structure from the original NMR ensemble of S4 delta41 and (b) the 1.7 Å crystal structure. In (a) and (b) the sheet- containing subdomain is in the same orientation, to emphasize both the similarity of the sheet- containing subdomains and the difference in the relative orien- tations of the helical subdomains. Elements of secondary structure and the chain termini are labeled. This Figure was generated with MOLSCRIPT (Kraulis, 1991).
Figure 5.
Figure 5. Stereoview of the sol- ution structure of S4 delta41, based on the NOE, hydrogen bond, dihedral angle, and N-H dipolar coupling restraints summarized in Table 1. The best 16 structures out of a cal- culation of 50 are shown in blue. For comparison, the crystal struc- ture is shown in magenta and the solution structure based on the original restraint list, lacking dipo- lar couplings, is shown in black. All structures are aligned by the backbone atoms in residues 94 to 176 (the sheet-containing subdo- main). Some residues at the ends of elements of secondary structure and the ends of the chain are labeled for reference.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 292, 375-387) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15340925 D.M.Standley, H.Toh, and H.Nakamura (2004).
Detecting local structural similarity in proteins by maximizing number of equivalent residues.
  Proteins, 57, 381-391.  
14718654 D.Zheng, J.M.Aramini, and G.T.Montelione (2004).
Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.
  Protein Sci, 13, 549-554.
PDB code: 1q2n
15754058 V.A.Higman, J.Boyd, L.J.Smith, and C.Redfield (2004).
Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings.
  J Biomol NMR, 30, 327-346.  
15298926 W.Li, Y.Zhang, and J.Skolnick (2004).
Application of sparse NMR restraints to large-scale protein structure prediction.
  Biophys J, 87, 1241-1248.  
14744980 Y.Qu, J.T.Guo, V.Olman, and Y.Xu (2004).
Protein structure prediction using sparse dipolar coupling data.
  Nucleic Acids Res, 32, 551-561.  
12837795 L.Volpon, C.Lievre, M.J.Osborne, S.Gandhi, P.Iannuzzi, R.Larocque, M.Cygler, K.Gehring, and I.Ekiel (2003).
The solution structure of YbcJ from Escherichia coli reveals a recently discovered alphaL motif involved in RNA binding.
  J Bacteriol, 185, 4204-4210.
PDB codes: 1o09 1p9k
11274458 H.Schwalbe, S.B.Grimshaw, A.Spencer, M.Buck, J.Boyd, C.M.Dobson, C.Redfield, and L.J.Smith (2001).
A refined solution structure of hen lysozyme determined using residual dipolar coupling data.
  Protein Sci, 10, 677-688.
PDB code: 1e8l
11063598 E.W.Sayers, R.B.Gerstner, D.E.Draper, and D.A.Torchia (2000).
Structural preordering in the N-terminal region of ribosomal protein S4 revealed by heteronuclear NMR spectroscopy.
  Biochemistry, 39, 13602-13613.  
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.