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PDBsum entry 3bbx

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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
3bbx
Jmol
Contents
Protein chains
94 a.a. *
267 a.a. *
209 a.a. *
201 a.a. *
178 a.a. *
176 a.a. *
149 a.a. *
140 a.a. *
121 a.a. *
144 a.a. *
136 a.a. *
127 a.a. *
117 a.a. *
114 a.a. *
117 a.a. *
103 a.a. *
110 a.a. *
99 a.a. *
102 a.a. *
84 a.a. *
63 a.a. *
58 a.a. *
70 a.a. *
56 a.a. *
54 a.a. *
46 a.a. *
64 a.a. *
38 a.a. *
DNA/RNA
Metals
_MG ×110
Waters ×506
* Residue conservation analysis
PDB id:
3bbx
Name: Ribosome
Title: The hsp15 protein fitted into the low resolution cryo-em map 50s.Nc-tRNA.Hsp15 complex
Structure: 5s ribosomal RNA. Chain: a. 23s ribosomal RNA. Chain: b. 50s ribosomal protein l25. Chain: v. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3.
Source: Escherichia coli. Organism_taxid: 562. Strain: mre600. Strain: mre600
Authors: L.Jiang,J.P.Abrahams
Key ref:
L.Jiang et al. (2008). Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Complexes by the Heat Shock Protein Hsp15. J Mol Biol, 386, 1357-1367. PubMed id: 19013177 DOI: 10.1016/j.jmb.2008.10.079
Date:
11-Nov-07     Release date:   21-Oct-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25
Seq:
Struc:
94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P60422  (RL2_ECOLI) -  50S ribosomal protein L2
Seq:
Struc:
273 a.a.
267 a.a.
Protein chain
Pfam   ArchSchema ?
P60438  (RL3_ECOLI) -  50S ribosomal protein L3
Seq:
Struc:
209 a.a.
209 a.a.
Protein chain
Pfam   ArchSchema ?
P60723  (RL4_ECOLI) -  50S ribosomal protein L4
Seq:
Struc:
201 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
P62399  (RL5_ECOLI) -  50S ribosomal protein L5
Seq:
Struc:
179 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG55  (RL6_ECOLI) -  50S ribosomal protein L6
Seq:
Struc:
177 a.a.
176 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9
Seq:
Struc:
149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P0AA10  (RL13_ECOLI) -  50S ribosomal protein L13
Seq:
Struc:
142 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY3  (RL14_ECOLI) -  50S ribosomal protein L14
Seq:
Struc:
123 a.a.
121 a.a.
Protein chain
Pfam   ArchSchema ?
P02413  (RL15_ECOLI) -  50S ribosomal protein L15
Seq:
Struc:
144 a.a.
144 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY7  (RL16_ECOLI) -  50S ribosomal protein L16
Seq:
Struc:
136 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG44  (RL17_ECOLI) -  50S ribosomal protein L17
Seq:
Struc:
127 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P0C018  (RL18_ECOLI) -  50S ribosomal protein L18
Seq:
Struc:
117 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19
Seq:
Struc:
115 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L3  (RL20_ECOLI) -  50S ribosomal protein L20
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG48  (RL21_ECOLI) -  50S ribosomal protein L21
Seq:
Struc:
103 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
P61175  (RL22_ECOLI) -  50S ribosomal protein L22
Seq:
Struc:
110 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ0  (RL23_ECOLI) -  50S ribosomal protein L23
Seq:
Struc:
100 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P60624  (RL24_ECOLI) -  50S ribosomal protein L24
Seq:
Struc:
104 a.a.
102 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29
Seq:
Struc:
63 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG51  (RL30_ECOLI) -  50S ribosomal protein L30
Seq:
Struc:
59 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M9  (RL31_ECOLI) -  50S ribosomal protein L31
Seq:
Struc:
70 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N4  (RL32_ECOLI) -  50S ribosomal protein L32
Seq:
Struc:
57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N9  (RL33_ECOLI) -  50S ribosomal protein L33
Seq:
Struc:
55 a.a.
54 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7P5  (RL34_ECOLI) -  50S ribosomal protein L34
Seq:
Struc:
46 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q1  (RL35_ECOLI) -  50S ribosomal protein L35
Seq:
Struc:
65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q6  (RL36_ECOLI) -  50S ribosomal protein L36
Seq:
Struc:
38 a.a.
38 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     response to antibiotic   8 terms 
  Biochemical function     structural constituent of ribosome     13 terms  

 

 
DOI no: 10.1016/j.jmb.2008.10.079 J Mol Biol 386:1357-1367 (2008)
PubMed id: 19013177  
 
 
Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Complexes by the Heat Shock Protein Hsp15.
L.Jiang, C.Schaffitzel, R.Bingel-Erlenmeyer, N.Ban, P.Korber, R.I.Koning, D.C.de Geus, J.R.Plaisier, J.P.Abrahams.
 
  ABSTRACT  
 
When heat shock prematurely dissociates a translating bacterial ribosome, its 50S subunit is prevented from reinitiating protein synthesis by tRNA covalently linked to the unfinished protein chain that remains threaded through the exit tunnel. Hsp15, a highly upregulated bacterial heat shock protein, reactivates such dead-end complexes. Here, we show with cryo-electron microscopy reconstructions and functional assays that Hsp15 translocates the tRNA moiety from the A site to the P site of stalled 50S subunits. By stabilizing the tRNA in the P site, Hsp15 indirectly frees up the A site, allowing a release factor to land there and cleave off the tRNA. Such a release factor must be stop codon independent, suggesting a possible role for a poorly characterized class of putative release factors that are upregulated by cellular stress, lack a codon recognition domain and are conserved in eukaryotes.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Rescue cycle of the stalled ribosomal 50S subunit. Heat shock can erroneously dissociate a translating ribosome into a 30S subunit and a blocked 50S subunit carrying a tRNA linked to the unfinished nascent chain (lower right). Here, we show that in these stalled 50S·nc-tRNA complexes, the tRNA is located at the A site (bottom right) and that the small heat shock protein Hsp15 translocates the tRNA to the P site (bottom left), where it can be liberated by a release factor (top left).
Figure 3.
Fig. 3. Reconstructions of (a) the 50S·nc-tRNA complex (the density of tRNA is in cyan, 14-Å resolution) and (b) the 50S·nc-tRNA·Hsp15 complex (the density of tRNA is in cyan and that of Hsp15 is in blue, 10-Å resolution). The central protuberance (CP), the L1 and L7/L12 domains and the P and A sites are indicated.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 386, 1357-1367) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21059683 O.René, and J.H.Alix (2011).
Late steps of ribosome assembly in E. coli are sensitive to a severe heat stress but are assisted by the HSP70 chaperone machine.
  Nucleic Acids Res, 39, 1855-1867.  
20639334 A.Rasouly, C.Davidovich, and E.Z.Ron (2010).
The heat shock protein YbeY is required for optimal activity of the 30S ribosomal subunit.
  J Bacteriol, 192, 4592-4596.  
20598281 H.Antonicka, E.Ostergaard, F.Sasarman, W.Weraarpachai, F.Wibrand, A.M.Pedersen, R.J.Rodenburg, M.S.van der Knaap, J.A.Smeitink, Z.M.Chrzanowska-Lightowlers, and E.A.Shoubridge (2010).
Mutations in C12orf65 in patients with encephalomyopathy and a mitochondrial translation defect.
  Am J Hum Genet, 87, 115-122.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
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.