PDBsum entry 2aar

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protein dna_rna links
Ribosome PDB id
Protein chains
93 a.a.* *
65 a.a.* *
113 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
Name: Ribosome
Title: Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome.
Structure: 23s ribosomal RNA. Chain: 0. 50s ribosomal protein l23. Chain: r. 50s ribosomal protein l29. Chain: w. Trigger factor. Chain: 7. Fragment: n-terminal domain.
Source: Deinococcus radiodurans. Organism_taxid: 1299. Organism_taxid: 1299
Biol. unit: Tetramer (from PQS)
3.50Å     R-factor:   0.251     R-free:   0.320
Authors: D.Baram,E.Pyetan,A.Sittner,T.Auerbach-Nevo,A.Bashan,A.Yonath
Key ref:
D.Baram et al. (2005). Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action. Proc Natl Acad Sci U S A, 102, 12017-12022. PubMed id: 16091460 DOI: 10.1073/pnas.0505581102
14-Jul-05     Release date:   23-Aug-05    

Protein chain
Pfam   ArchSchema ?
Q9RXK0  (RL23_DEIRA) -  50S ribosomal protein L23
95 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
Q9RXJ4  (RL29_DEIRA) -  50S ribosomal protein L29
67 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
Q9RT21  (TIG_DEIRA) -  Trigger factor
465 a.a.
113 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chain 7: E.C.  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   3 terms 
  Biological process     protein transport   3 terms 
  Biochemical function     nucleotide binding     4 terms  


    Added reference    
DOI no: 10.1073/pnas.0505581102 Proc Natl Acad Sci U S A 102:12017-12022 (2005)
PubMed id: 16091460  
Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action.
D.Baram, E.Pyetan, A.Sittner, T.Auerbach-Nevo, A.Bashan, A.Yonath.
Trigger factor (TF), the first chaperone in eubacteria to encounter the emerging nascent chain, binds to the large ribosomal subunit in the vicinity of the protein exit tunnel opening and forms a sheltered folding space. Here, we present the 3.5-A crystal structure of the physiological complex of the large ribosomal subunit from the eubacterium Deinococcus radiodurans with the N-terminal domain of TF (TFa) from the same organism. For anchoring, TFa exploits a small ribosomal surface area in the vicinity of proteins L23 and L29, by using its "signature motif" as well as additional structural elements. The molecular details of TFa interactions reveal that L23 is essential for the association of TF with the ribosome and may serve as a channel of communication with the nascent chain progressing in the tunnel. L29 appears to induce a conformational change in TFa, which results in the exposure of TFa hydrophobic patches to the opening of the ribosomal exit tunnel, thus increasing its affinity for hydrophobic segments of the emerging nascent polypeptide. This observation implies that, in addition to creating a protected folding space for the emerging nascent chain, TF association with the ribosome prevents aggregation by providing a competing hydrophobic environment and may be critical for attaining the functional conformation necessary for chaperone activity.
  Selected figure(s)  
Figure 2.
Fig. 2. The crystallographic structure of bound TFa. (a) Structure of TFa upon association with the ribosome. (b) An unbiased 2F[o] - F[c] electron density map around helix A1, contoured at 1.5 .
Figure 4.
Fig. 4. Detailed molecular interactions of TFa (orange) with ribosomal proteins L23 (blue) (a and b) and L29 (magenta) (c).
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21370971 D.V.Fedyukina, and S.Cavagnero (2011).
Protein folding at the exit tunnel.
  Annu Rev Biophys, 40, 337-359.  
20797628 F.Brandt, L.A.Carlson, F.U.Hartl, W.Baumeister, and K.Grünewald (2010).
The three-dimensional organization of polyribosomes in intact human cells.
  Mol Cell, 39, 560-569.  
19809489 A.Hoffmann, and B.Bukau (2009).
Trigger factor finds new jobs and contacts.
  Nat Struct Mol Biol, 16, 1006-1008.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
19647435 C.Giglione, S.Fieulaine, and T.Meinnel (2009).
Cotranslational processing mechanisms: towards a dynamic 3D model.
  Trends Biochem Sci, 34, 417-426.  
19167328 F.Brandt, S.A.Etchells, J.O.Ortiz, A.H.Elcock, F.U.Hartl, and W.Baumeister (2009).
The native 3D organization of bacterial polysomes.
  Cell, 136, 261-271.  
19491934 F.U.Hartl, and M.Hayer-Hartl (2009).
Converging concepts of protein folding in vitro and in vivo.
  Nat Struct Mol Biol, 16, 574-581.  
19491936 G.Kramer, D.Boehringer, N.Ban, and B.Bukau (2009).
The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins.
  Nat Struct Mol Biol, 16, 589-597.  
19029307 I.A.Buskiewicz, J.Jöckel, M.V.Rodnina, and W.Wintermeyer (2009).
Conformation of the signal recognition particle in ribosomal targeting complexes.
  RNA, 15, 44-54.  
19569194 J.P.Ellis, P.H.Culviner, and S.Cavagnero (2009).
Confined dynamics of a ribosome-bound nascent globin: Cone angle analysis of fluorescence depolarization decays in the presence of two local motions.
  Protein Sci, 18, 2003-2015.  
18497744 F.Merz, D.Boehringer, C.Schaffitzel, S.Preissler, A.Hoffmann, T.Maier, A.Rutkowska, J.Lozza, N.Ban, B.Bukau, and E.Deuerling (2008).
Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.
  EMBO J, 27, 1622-1632.
PDB code: 2vrh
  18717565 J.P.Ellis, C.K.Bakke, R.N.Kirchdoerfer, L.M.Jungbauer, and S.Cavagnero (2008).
Chain dynamics of nascent polypeptides emerging from the ribosome.
  ACS Chem Biol, 3, 555-566.  
18829863 K.Peisker, D.Braun, T.Wölfle, J.Hentschel, U.Fünfschilling, G.Fischer, A.Sickmann, and S.Rospert (2008).
Ribosome-associated complex binds to ribosomes in close proximity of Rpl31 at the exit of the polypeptide tunnel in yeast.
  Mol Biol Cell, 19, 5279-5288.  
18400172 M.Selmer, and A.Liljas (2008).
Exit biology: battle for the nascent chain.
  Structure, 16, 498-500.  
17584789 C.L.Ross, R.R.Patel, T.C.Mendelson, and V.C.Ware (2007).
Functional conservation between structurally diverse ribosomal proteins from Drosophila melanogaster and Saccharomyces cerevisiae: fly L23a can substitute for yeast L25 in ribosome assembly and function.
  Nucleic Acids Res, 35, 4503-4514.  
17372359 E.Martinez-Hackert, and W.A.Hendrickson (2007).
Structures of and interactions between domains of trigger factor from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 63, 536-547.
PDB codes: 2nsa 2nsb 2nsc
17525465 Y.Shi, D.J.Fan, S.X.Li, H.J.Zhang, S.Perrett, and J.M.Zhou (2007).
Identification of a potential hydrophobic peptide binding site in the C-terminal arm of trigger factor.
  Protein Sci, 16, 1165-1175.  
17122845 A.Yonath (2006).
Molecular biology: triggering positive competition.
  Nature, 444, 435-436.  
17051157 C.M.Kaiser, H.C.Chang, V.R.Agashe, S.K.Lakshmipathy, S.A.Etchells, M.Hayer-Hartl, F.U.Hartl, and J.M.Barral (2006).
Real-time observation of trigger factor function on translating ribosomes.
  Nature, 444, 455-460.  
16317791 D.W.Heinz, M.S.Weiss, and K.U.Wendt (2006).
Biomacromolecular interactions, assemblies and machines: a structural view.
  Chembiochem, 7, 203-208.  
16421445 H.Kettenberger, and P.Cramer (2006).
Fluorescence detection of nucleic acids and proteins in multi-component crystals.
  Acta Crystallogr D Biol Crystallogr, 62, 146-150.  
16336118 D.N.Wilson, J.M.Harms, K.H.Nierhaus, F.Schlünzen, and P.Fucini (2005).
Species-specific antibiotic-ribosome interactions: implications for drug development.
  Biol Chem, 386, 1239-1252.  
16271881 J.H.Cate (2005).
The ins and outs of protein synthesis.
  Structure, 13, 1584-1585.  
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.