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PDBsum entry 1cjs

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protein links
Ribosome PDB id
1cjs
Jmol
Contents
Protein chain
213 a.a. *
Waters ×70
* Residue conservation analysis
PDB id:
1cjs
Name: Ribosome
Title: Crystal structure of ribosomal protein l1 from methanococcus jannaschii
Structure: 50s ribosomal protein l1p. Chain: a. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: rpla. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.30Å     R-factor:   0.203     R-free:   0.271
Authors: N.Nevskaya,S.Tishchenko,R.Fedorov,S.Al-Karadaghi,A.Liljas, A.Kraft,W.Piendl,M.Garber,S.Nikonov
Key ref:
N.Nevskaya et al. (2000). Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family. Structure, 8, 363-371. PubMed id: 10801481 DOI: 10.1016/S0969-2126(00)00116-7
Date:
19-Apr-99     Release date:   31-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P54050  (RL1_METJA) -  50S ribosomal protein L1
Seq:
Struc:
219 a.a.
213 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ribonucleoprotein complex   3 terms 
  Biological process     regulation of translation   2 terms 
  Biochemical function     structural constituent of ribosome     4 terms  

 

 
DOI no: 10.1016/S0969-2126(00)00116-7 Structure 8:363-371 (2000)
PubMed id: 10801481  
 
 
Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family.
N.Nevskaya, S.Tischenko, R.Fedorov, S.Al-Karadaghi, A.Liljas, A.Kraft, W.Piendl, M.Garber, S.Nikonov.
 
  ABSTRACT  
 
BACKGROUND: L1 is an important primary rRNA-binding protein, as well as a translational repressor that binds mRNA. It was shown that L1 proteins from some bacteria and archaea are functionally interchangeable within the ribosome and in the repression of translation. The crystal structure of bacterial L1 from Thermus thermophilus (TthL1) has previously been determined. RESULTS: We report here the first structure of a ribosomal protein from archaea, L1 from Methanococcus jannaschii (MjaL1). The overall shape of the two-domain molecule differs dramatically from that of its bacterial counterpart (TthL1) because of the different relative orientations of the domains. Two strictly conserved regions of the amino acid sequence, each belonging to one of the domains and positioned close to each other in the interdomain cavity of TthL1, are separated by about 25 A in MjaL1 owing to a significant opening of the structure. These regions are structurally highly conserved and are proposed to be the specific RNA-binding sites. CONCLUSIONS: The unusually high RNA-binding affinity of MjaL1 might be explained by the exposure of its highly conserved regions. The open conformation of MjaL1 is strongly stabilized by nonconserved interdomain interactions and suggests that the closed conformations of L1 (as in TthL1) open upon RNA binding. Comparison of the two L1 protein structures reveals a high conformational variability of this ribosomal protein. Determination of the MjaL1 structure offers an additional variant for fitting the L1 protein into electron-density maps of the 50S ribosomal subunit.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. The molecular surfaces of (a) TthL1 and (b) MjaL1 coloured by electrostatic potential (red, negative; blue, positive; white, uncharged). A well-defined region of positive charge is seen clearly in domain II of MjaL1. (This figure was generated using WebLab ViewerPro [29].)

 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 363-371) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20740692 O.Kostareva, S.Tishchenko, E.Nikonova, V.Kljashtorny, N.Nevskaya, A.Nikulin, A.Sycheva, S.Moshkovskii, W.Piendl, M.Garber, and S.Nikonov (2011).
Disruption of shape complementarity in the ribosomal protein L1-RNA contact region does not hinder specific recognition of the RNA target site.
  J Mol Recognit, 24, 524-532.  
17981968 C.Wicker-Planquart, A.E.Foucher, M.Louwagie, R.A.Britton, and J.M.Jault (2008).
Interactions of an essential Bacillus subtilis GTPase, YsxC, with ribosomes.
  J Bacteriol, 190, 681-690.  
17962298 S.Tishchenko, E.Nikonova, V.Kljashtorny, O.Kostareva, N.Nevskaya, W.Piendl, N.Davydova, V.Streltsov, M.Garber, and S.Nikonov (2007).
Domain I of ribosomal protein L1 is sufficient for specific RNA binding.
  Nucleic Acids Res, 35, 7389-7395.
PDB codes: 2oum 2ov7
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
15339800 K.Réblová, N.Spacková, J.Koca, N.B.Leontis, and J.Sponer (2004).
Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.
  Biophys J, 87, 3397-3412.  
12514741 A.Nikulin, I.Eliseikina, S.Tishchenko, N.Nevskaya, N.Davydova, O.Platonova, W.Piendl, M.Selmer, A.Liljas, D.Drygin, R.Zimmermann, M.Garber, and S.Nikonov (2003).
Structure of the L1 protuberance in the ribosome.
  Nat Struct Biol, 10, 104-108.
PDB code: 1mzp
12887894 H.K.Song, and M.J.Eck (2003).
Structural basis of degradation signal recognition by SspB, a specificity-enhancing factor for the ClpXP proteolytic machine.
  Mol Cell, 12, 75-86.
PDB codes: 1ox8 1ox9
12037305 N.Nevskaya, S.Tishchenko, M.Paveliev, Y.Smolinskaya, R.Fedorov, W.Piendl, Y.Nakamura, T.Toyoda, M.Garber, and S.Nikonov (2002).
Structure of ribosomal protein L1 from Methanococcus thermolithotrophicus. Functionally important structural invariants on the L1 surface.
  Acta Crystallogr D Biol Crystallogr, 58, 1023-1029.
PDB code: 1dwu
11142372 D.Drygin, and R.A.Zimmermann (2000).
Magnesium ions mediate contacts between phosphoryl oxygens at positions 2122 and 2176 of the 23S rRNA and ribosomal protein L1.
  RNA, 6, 1714-1726.  
10937989 N.Ban, P.Nissen, J.Hansen, P.B.Moore, and T.A.Steitz (2000).
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
  Science, 289, 905-920.
PDB code: 1ffk
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.