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PDBsum entry 2d3o

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
2d3o
Jmol
Contents
Protein chains
93 a.a. *
110 a.a. *
66 a.a. *
100 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
2d3o
Name: Ribosome
Title: Structure of ribosome binding domain of the trigger factor on the 50s ribosomal subunit from d. Radiodurans
Structure: 23s ribosomal RNA. Chain: 0. 50s ribosomal protein l23. Chain: r. 50s ribosomal protein l24. Chain: s. 50s ribosomal protein l29. Chain: w. Trigger factor.
Source: Deinococcus radiodurans. Organism_taxid: 1299. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Pentamer (from PQS)
Resolution:
3.35Å     R-factor:   0.299     R-free:   0.322
Authors: F.Schluenzen,D.N.Wilson,H.A.Hansen,P.Tian,J.M.Harms, S.J.Mcinnes,R.Albrecht,J.Buerger,S.M.Wilbanks,P.Fucini
Key ref:
F.Schlünzen et al. (2005). The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction. Structure (Camb), 13, 1685-1694. PubMed id: 16271892 DOI: 10.1016/j.str.2005.08.007
Date:
30-Sep-05     Release date:   06-Dec-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9RXK0  (RL23_DEIRA) -  50S ribosomal protein L23
Seq:
Struc:
95 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
Q9RXJ1  (RL24_DEIRA) -  50S ribosomal protein L24
Seq:
Struc:
115 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
Q9RXJ4  (RL29_DEIRA) -  50S ribosomal protein L29
Seq:
Struc:
67 a.a.
66 a.a.
Protein chain
Pfam   ArchSchema ?
Q9RT21  (TIG_DEIRA) -  Trigger factor
Seq:
Struc:
465 a.a.
100 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain 1: E.C.5.2.1.8  - 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: 10.1016/j.str.2005.08.007 Structure (Camb) 13:1685-1694 (2005)
PubMed id: 16271892  
 
 
The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction.
F.Schlünzen, D.N.Wilson, P.Tian, J.M.Harms, S.J.McInnes, H.A.Hansen, R.Albrecht, J.Buerger, S.M.Wilbanks, P.Fucini.
 
  ABSTRACT  
 
This study presents the X-ray structure of the N-terminal binding domain of the D. radiodurans trigger factor (TF) in complex with the D. radiodurans large ribosomal subunit. At 3.35 A, a complete description of the interactions with ribosomal proteins L23, L29, and 23S rRNA are disclosed, many of which differ from those found previously for a heterologous bacterial-archaeal TF-ribosome complex. The beta hairpin loop of eubacterial L24, which is shorter in archaeal ribosomes, contacts the TF and severely diminishes the molecular cradle proposed to exist between the TF and ribosome. Bound to the ribosome, TF exposes a hydrophobic crevice large enough to accommodate the nascent polypeptide chain. Superimposition of the full-length TF and the signal-recognition particle (SRP) onto the complex shows that simultaneous cohabitation is possible, in agreement with biochemical data, and suggests a model for the interplay of TF, SRP, and the nascent chain during translation.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Model for Interplay between the TF, SRP, and the Nascent Chain during Translation
Schematic view of the bottom of the ribosome, showing ribosomal proteins L23, (green), L24 (yellow), and L29 (orange), and with the tunnel exit site indicated with an arrow. (A) TF is the first chaperone to bind to the bacterial ribosome as the nascent chain emerges from the tunnel. Direct contact between L24 and the TF results in conformational changes in the TF-BD that expose a hydrophobic crevice located in the TF-BD, through which the polypeptide chain can pass. (B) The SRP particle binds to the ribosome in the presence of the TF, initially through contacts with L29. The M domain of the SRP covers the hydrophobic cavity in the TF-BD and monitors for the presence of a signal sequence in the nascent chain. (C) Interaction between the signal sequence-containing nascent chain and the M domain of the SRP enables the M domain to establish contact with H24 of the 23S rRNA. This interaction stabilizes the SRP particle on the ribosome and could lead to dissociation of the TF. (D) In the absence of a signal sequence, the M domain cannot establish contact with the 23S rRNA, and the SRP dissociates from the ribosome. Continued translation leads to elongation of the nascent chain, which is channeled through the hydrophobic cavity into the central cavity (body) of the TF. The restricted size of the cavity due to the presence of L24 limits the possibility for folding of entire protein domains. The PPIase domain (head) of the TF may recognize the nascent chain as it emerges from the head side, monitoring for proline residues that need to be isomerized (arrowed).
 
  The above figure is reprinted by permission from Cell Press: Structure (Camb) (2005, 13, 1685-1694) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
19702336 J.L.Miller, H.Cimen, H.Koc, and E.C.Koc (2009).
Phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis.
  J Proteome Res, 8, 4789-4798.  
19087962 O.O.Panasenko, F.P.David, and M.A.Collart (2009).
Ribosome association and stability of the nascent polypeptide-associated complex is dependent upon its own ubiquitination.
  Genetics, 181, 447-460.  
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
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.  
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
  Nat Rev Mol Cell Biol, 9, 242-253.  
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
17296610 S.K.Lakshmipathy, S.Tomic, C.M.Kaiser, H.C.Chang, P.Genevaux, C.Georgopoulos, J.M.Barral, A.E.Johnson, F.U.Hartl, and S.A.Etchells (2007).
Identification of nascent chain interaction sites on trigger factor.
  J Biol Chem, 282, 12186-12193.  
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.  
16407311 A.Hoffmann, F.Merz, A.Rutkowska, B.Zachmann-Brand, E.Deuerling, and B.Bukau (2006).
Trigger factor forms a protective shield for nascent polypeptides at the ribosome.
  J Biol Chem, 281, 6539-6545.  
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.  
16421097 G.Eisner, M.Moser, U.Schäfer, K.Beck, and M.Müller (2006).
Alternate recruitment of signal recognition particle and trigger factor to the signal sequence of a growing nascent polypeptide.
  J Biol Chem, 281, 7172-7179.  
17086193 M.Halic, M.Blau, T.Becker, T.Mielke, M.R.Pool, K.Wild, I.Sinning, and R.Beckmann (2006).
Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
  Nature, 444, 507-511.
PDB codes: 2j28 2j37
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.