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PDBsum entry 2vrh

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protein links
Ribosome PDB id
2vrh
Jmol
Contents
Protein chains
431 a.a.* *
99 a.a.* *
102 a.a.* *
63 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
2vrh
Name: Ribosome
Title: Structure of the e. Coli trigger factor bound to a translating ribosome
Structure: Trigger factor. Chain: a. Engineered: yes. Other_details: based on PDB 1w26_a. Residues 22-62 were replaced with the corresponding residues of PDB 1oms_b. 50s ribosomal protein l23. Chain: b. Other_details: based on PDB 2aw4_t. 50s ribosomal protein l24.
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: based on PDB 1w26_a. Other_details: based on PDB 2aw4_t. Other_details: based on PDB 2aw4_u. Other_details: based on PDB 2aw4_x
Authors: F.Merz,D.Boehringer,C.Schaffitzel,S.Preissler,A.Hoffmann, T.Maier,A.Rutkowska,J.Lozza,N.Ban,B.Bukau,E.Deuerling
Key ref: F.Merz et al. (2008). Molecular mechanism and structure of Trigger Factor bound to the translating ribosome. EMBO J, 27, 1622-1632. PubMed id: 18497744
Date:
07-Apr-08     Release date:   17-Jun-08    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A850  (TIG_ECOLI) -  Trigger factor
Seq:
Struc:
432 a.a.
431 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 ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29
Seq:
Struc:
63 a.a.
63 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chain A: 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     membrane   7 terms 
  Biological process     cell cycle   8 terms 
  Biochemical function     protein binding involved in protein folding     10 terms  

 

 
    Added reference    
 
 
EMBO J 27:1622-1632 (2008)
PubMed id: 18497744  
 
 
Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.
F.Merz, D.Boehringer, C.Schaffitzel, S.Preissler, A.Hoffmann, T.Maier, A.Rutkowska, J.Lozza, N.Ban, B.Bukau, E.Deuerling.
 
  ABSTRACT  
 
Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome-nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors.
 

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.  
20439768 C.Eichmann, S.Preissler, R.Riek, and E.Deuerling (2010).
Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy.
  Proc Natl Acad Sci U S A, 107, 9111-9116.  
20067623 C.Varela, C.Mauriaca, A.Paradela, J.P.Albar, C.A.Jerez, and F.P.Chávez (2010).
New structural and functional defects in polyphosphate deficient bacteria: a cellular and proteomic study.
  BMC Microbiol, 10, 7.  
20371331 K.G.Ugrinov, and P.L.Clark (2010).
Cotranslational folding increases GFP folding yield.
  Biophys J, 98, 1312-1320.  
19809489 A.Hoffmann, and B.Bukau (2009).
Trigger factor finds new jobs and contacts.
  Nat Struct Mol Biol, 16, 1006-1008.  
19647435 C.Giglione, S.Fieulaine, and T.Meinnel (2009).
Cotranslational processing mechanisms: towards a dynamic 3D model.
  Trends Biochem Sci, 34, 417-426.  
19737520 E.Martinez-Hackert, and W.A.Hendrickson (2009).
Promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone.
  Cell, 138, 923-934.
PDB codes: 3gty 3gu0
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.  
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.  
19725877 L.Marcellini, M.Borro, G.Gentile, A.C.Rinaldi, L.Stella, P.Aimola, D.Barra, and M.L.Mangoni (2009).
Esculentin-1b(1-18)--a membrane-active antimicrobial peptide that synergizes with antibiotics and modifies the expression level of a limited number of proteins in Escherichia coli.
  FEBS J, 276, 5647-5664.  
19173718 O.Kolaj, S.Spada, S.Robin, and J.G.Wall (2009).
Use of folding modulators to improve heterologous protein production in Escherichia coli.
  Microb Cell Fact, 8, 9.  
19450532 R.Kohler, D.Boehringer, B.Greber, R.Bingel-Erlenmeyer, I.Collinson, C.Schaffitzel, and N.Ban (2009).
YidC and Oxa1 form dimeric insertion pores on the translating ribosome.
  Mol Cell, 34, 344-353.  
19060145 S.Robin, D.M.Togashi, A.G.Ryder, and J.G.Wall (2009).
Trigger factor from the psychrophilic bacterium Psychrobacter frigidicola is a monomeric chaperone.
  J Bacteriol, 191, 1162-1168.  
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.