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protein dna_rna links
RNA binding protein/RNA PDB id
1zc8
Jmol
Contents
Protein chains
130 a.a.* *
405 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
1zc8
Name: RNA binding protein/RNA
Title: Coordinates of tmrna, smpb, ef-tu and h44 fitted into cryo- em map of the 70s ribosome and tmrna complex
Structure: Tld 16s ribosomal RNA. Chain: a. H2 16s rrna. Chain: b. H2b d mRNA. Chain: c. Protein kinase 4 mRNA. Chain: g. Other_details: pk1.
Source: Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
Authors: M.Valle,R.Gillet,S.Kaur,A.Henne,V.Ramakrishnan,J.Frank
Key ref:
M.Valle et al. (2003). Visualizing tmRNA entry into a stalled ribosome. Science, 300, 127-130. PubMed id: 12677067 DOI: 10.1126/science.1081798
Date:
11-Apr-05     Release date:   19-Apr-05    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O66640  (SSRP_AQUAE) -  SsrA-binding protein
Seq:
Struc: 		157 a.a.
130 a.a.
Protein chain
Pfam   ArchSchema ?
P60338  (EFTU1_THETH) -  Elongation factor Tu-A
Seq:
Struc: 		406 a.a.
405 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 10 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     translation   2 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1126/science.1081798 Science 300:127-130 (2003)
PubMed id: 12677067  
 
 
Visualizing tmRNA entry into a stalled ribosome.
M.Valle, R.Gillet, S.Kaur, A.Henne, V.Ramakrishnan, J.Frank.
 
  ABSTRACT  
 
Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation then switches from the defective message to a short open reading frame on tmRNA that tags the defective nascent peptide chain for degradation. However, the mechanism by which tmRNA can enter and move through the ribosome is unknown. We present a cryo-electron microscopy study at approximately 13 to 15 angstroms of the entry of tmRNA into the ribosome. The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Secondary structure diagram of tmRNA. Base pairs are linked by lines, whereas GU pairs are represented by dots. The TLD, the four pseudoknots (PK1 to PK4), and helices (numbered from 1 to 12) are shown in the colors that are used to represent these modules in subsequent figures. The nucleotides within the ORF are shown in a larger font. T. thermophilus sequence numbers are shown, with the corresponding E. coli numbering in parentheses. The figure is adapted from the diagram for E. coli on the tmRDB Web site (29, 41). 		Figure 4.
Fig. 4. Comparison of maps of tmRNA complexes with and without S1. Cryo-EM maps for the 70S tRNA EF-Tu tmRNA SmpB complex in the presence (A) and absence (B) of ribosomal protein S1. Different colors for the density attributable to EF-Tu tmRNA SmpB are used to allow a comparison in (C), where the purple semitransparent map from (B) is depicted together with the solid red from (A). In the absence of S1 (B) an additional connection is seen between PK1 and helix H5 of the tmRNA (D) that reveals the presence of the folded ORF.
 
  The above figures are reprinted by permission from the AAAs: Science (2003, 300, 127-130) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21081960 B.P.Klaholz (2010).
Let's see how tmRNA rescues a stuck ribosome.
  EMBO J, 29, 3747-3749.  
19914241 C.S.Hayes, and K.C.Keiler (2010).
Beyond ribosome rescue: tmRNA and co-translational processes.
  FEBS Lett, 584, 413-419.  
20348441 D.Kurita, A.Muto, and H.Himeno (2010).
Role of the C-terminal tail of SmpB in the early stage of trans-translation.
  RNA, 16, 980-990.  
20953161 F.Weis, P.Bron, E.Giudice, J.P.Rolland, D.Thomas, B.Felden, and R.Gillet (2010).
tmRNA-SmpB: a journey to the centre of the bacterial ribosome.
  EMBO J, 29, 3810-3818.
PDB codes: 3iyq 3iyr
20038631 F.Weis, P.Bron, J.P.Rolland, D.Thomas, B.Felden, and R.Gillet (2010).
Accommodation of tmRNA-SmpB into stalled ribosomes: a cryo-EM study.
  RNA, 16, 299-306.  
20487556 H.Hartman, and T.F.Smith (2010).
GTPases and the origin of the ribosome.
  Biol Direct, 5, 36.  
20940705 J.Fu, Y.Hashem, I.Wower, J.Lei, H.Y.Liao, C.Zwieb, J.Wower, and J.Frank (2010).
Visualizing the transfer-messenger RNA as the ribosome resumes translation.
  EMBO J, 29, 3819-3825.
PDB code: 3iz4
19925844 S.Shoji, B.D.Janssen, C.S.Hayes, and K.Fredrick (2010).
Translation factor LepA contributes to tellurite resistance in Escherichia coli but plays no apparent role in the fidelity of protein synthesis.
  Biochimie, 92, 157-163.  
20004164 A.Matsumoto, and H.Ishida (2009).
Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures.
  Structure, 17, 1605-1613.  
19861420 E.Y.Bugaeva, S.Surkov, A.V.Golovin, L.G.Ofverstedt, U.Skoglund, L.A.Isaksson, A.A.Bogdanov, O.V.Shpanchenko, and O.A.Dontsova (2009).
Structural features of the tmRNA-ribosome interaction.
  RNA, 15, 2312-2320.  
19001120 I.K.Wower, C.Zwieb, and J.Wower (2009).
Escherichia coli tmRNA lacking pseudoknot 1 tags truncated proteins in vivo and in vitro.
  RNA, 15, 128-137.  
19417362 J.M.Yuk, T.W.Kim, J.Y.Lee, Y.S.No, D.H.Kim, W.K.Choi, and S.Jin (2009).
The creation of sub-10 nm In(PO3)3 nanocrystals in an insulating matrix, and underlying formation mechanisms.
  Nanotechnology, 20, 55703.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
19132006 S.Nonin-Lecomte, N.Germain-Amiot, R.Gillet, M.Hallier, L.Ponchon, F.Dardel, and B.Felden (2009).
Ribosome hijacking: a role for small protein B during trans-translation.
  EMBO Rep, 10, 160-165.  
18598387 J.Wower, I.K.Wower, and C.Zwieb (2008).
Making the jump: new insights into the mechanism of trans-translation.
  J Biol, 7, 17.  
18557701 K.C.Keiler (2008).
Biology of trans-translation.
  Annu Rev Microbiol, 62, 133-151.  
18306177 K.Mikulík, P.Palecková, J.Felsberg, J.Bobek, J.Zídková, and P.Halada (2008).
SsrA genes of streptomycetes and association of proteins to the tmRNA during development and cellular differentiation.
  Proteomics, 8, 1429-1441.  
18648069 L.Metzinger, M.Hallier, and B.Felden (2008).
The highest affinity binding site of small protein B on transfer messenger RNA is outside the tRNA domain.
  RNA, 14, 1761-1772.  
18849406 M.Orzechowski, and F.Tama (2008).
Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations.
  Biophys J, 95, 5692-5705.  
18590561 M.R.Miller, D.W.Healey, S.G.Robison, J.D.Dewey, and A.R.Buskirk (2008).
The role of upstream sequences in selecting the reading frame on tmRNA.
  BMC Biol, 6, 29.  
17383929 K.C.Keiler (2007).
Physiology of tmRNA: what gets tagged and why?
  Curr Opin Microbiol, 10, 169-175.  
17299130 K.Takada, C.Takemoto, M.Kawazoe, T.Konno, K.Hanawa-Suetsugu, S.Lee, M.Shirouzu, S.Yokoyama, A.Muto, and H.Himeno (2007).
In vitro trans-translation of Thermus thermophilus: ribosomal protein S1 is not required for the early stage of trans-translation.
  RNA, 13, 503-510.  
17392345 M.Saguy, R.Gillet, P.Skorski, S.Hermann-Le Denmat, and B.Felden (2007).
Ribosomal protein S1 influences trans-translation in vitro and in vivo.
  Nucleic Acids Res, 35, 2368-2376.  
17400816 N.Ivanova, M.Lindell, M.Pavlov, L.Holmberg Schiavone, E.G.Wagner, and M.Ehrenberg (2007).
Structure probing of tmRNA in distinct stages of trans-translation.
  RNA, 13, 713-722.  
18205605 O.M.Selivanova, Y.Y.Fedorova, and I.N.Serduyk (2007).
Proteolysis of ribosomal protein S1 from Escherichia coli and Thermus thermophilus leads to formation of two different fragments.
  Biochemistry (Mosc), 72, 1225-1232.  
17291191 S.D.Moore, and R.T.Sauer (2007).
The tmRNA system for translational surveillance and ribosome rescue.
  Annu Rev Biochem, 76, 101-124.  
17911096 T.R.Sundermeier, and A.W.Karzai (2007).
Functional SmpB-ribosome interactions require tmRNA.
  J Biol Chem, 282, 34779-34786.  
17488812 Y.Bessho, R.Shibata, S.Sekine, K.Murayama, K.Higashijima, C.Hori-Takemoto, M.Shirouzu, S.Kuramitsu, and S.Yokoyama (2007).
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
  Proc Natl Acad Sci U S A, 104, 8293-8298.
PDB codes: 1wjx 2czj
16611927 M.Hallier, J.Desreac, and B.Felden (2006).
Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation.
  Nucleic Acids Res, 34, 1935-1943.  
17056712 S.Kaur, R.Gillet, W.Li, R.Gursky, and J.Frank (2006).
Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.
  Proc Natl Acad Sci U S A, 103, 16484-16489.  
16595798 S.Nonin-Lecomte, B.Felden, and F.Dardel (2006).
NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation.
  Nucleic Acids Res, 34, 1847-1853.
PDB code: 2g1w
16053518 A.Liiv, D.Karitkina, U.Maiväli, and J.Remme (2005).
Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis.
  BMC Mol Biol, 6, 18.  
15811920 I.K.Wower, C.Zwieb, and J.Wower (2005).
Transfer-messenger RNA unfolds as it transits the ribosome.
  RNA, 11, 668-673.  
15958166 J.Burks, C.Zwieb, F.Müller, I.Wower, and J.Wower (2005).
Comparative 3-D modeling of tmRNA.
  BMC Mol Biol, 6, 14.  
16261170 J.Poehlsgaard, and S.Douthwaite (2005).
The bacterial ribosome as a target for antibiotics.
  Nat Rev Microbiol, 3, 870-881.  
16204455 K.Asano, D.Kurita, K.Takada, T.Konno, A.Muto, and H.Himeno (2005).
Competition between trans-translation and termination or elongation of translation.
  Nucleic Acids Res, 33, 5544-5552.  
15860775 L.Metzinger, M.Hallier, and B.Felden (2005).
Independent binding sites of small protein B onto transfer-messenger RNA during trans-translation.
  Nucleic Acids Res, 33, 2384-2394.  
15972795 N.Ivanova, M.Y.Pavlov, E.Bouakaz, M.Ehrenberg, and L.H.Schiavone (2005).
Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA.
  Nucleic Acids Res, 33, 3529-3539.  
16174429 O.Llorca (2005).
Introduction to 3D reconstruction of macromolecules using single particle electron microscopy.
  Acta Pharmacol Sin, 26, 1153-1164.  
16194232 S.D.Moore, and R.T.Sauer (2005).
Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli.
  Mol Microbiol, 58, 456-466.  
15978085 S.J.Hong, Q.A.Tran, and K.C.Keiler (2005).
Cell cycle-regulated degradation of tmRNA is controlled by RNase R and SmpB.
  Mol Microbiol, 57, 565-575.  
15699355 T.R.Sundermeier, D.P.Dulebohn, H.J.Cho, and A.W.Karzai (2005).
A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation.
  Proc Natl Acad Sci U S A, 102, 2316-2321.  
15766524 T.T.Lee, S.Agarwalla, and R.M.Stroud (2005).
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.
  Cell, 120, 599-611.
PDB code: 2bh2
15465319 E.V.Orlova, and H.R.Saibil (2004).
Structure determination of macromolecular assemblies by single-particle analysis of cryo-electron micrographs.
  Curr Opin Struct Biol, 14, 584-590.  
15340139 K.E.McGinness, and R.T.Sauer (2004).
Ribosomal protein S1 binds mRNA and tmRNA similarly but plays distinct roles in translation of these molecules.
  Proc Natl Acad Sci U S A, 101, 13454-13459.  
15037763 K.Williams (2004).
Evolutionary resealing of a split RNA: Reversal of gene permutation.
  RNA, 10, 555-557.  
15571069 L.Kovács, K.Megyeri, A.Juhász, A.Zaja, and A.Miczák (2004).
Cloning, expression and purification of SmpB from Mycobacterium tuberculosis.
  Acta Microbiol Immunol Hung, 51, 297-302.  
15100436 M.J.Trimble, A.Minnicus, and K.P.Williams (2004).
tRNA slippage at the tmRNA resume codon.
  RNA, 10, 805-812.  
15102450 P.W.Haebel, S.Gutmann, and N.Ban (2004).
Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs.
  Curr Opin Struct Biol, 14, 58-65.  
15181002 S.Agarwalla, R.M.Stroud, and B.J.Gaffney (2004).
Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies.
  J Biol Chem, 279, 34123-34129.  
15487940 S.Gottesman (2004).
The small RNA regulators of Escherichia coli: roles and mechanisms*.
  Annu Rev Microbiol, 58, 303-328.  
15326226 S.M.Sharkady, and K.P.Williams (2004).
A third lineage with two-piece tmRNA.
  Nucleic Acids Res, 32, 4531-4538.  
15295039 T.Konno, T.Takahashi, D.Kurita, A.Muto, and H.Himeno (2004).
A minimum structure of aminoglycosides that causes an initiation shift of trans-translation.
  Nucleic Acids Res, 32, 4119-4126.  
15564671 T.Okada, I.K.Wower, J.Wower, C.W.Zwieb, and M.Kimura (2004).
Contribution of the second OB fold of ribosomal protein S1 from Escherichia coli to the recognition of TmRNA.
  Biosci Biotechnol Biochem, 68, 2319-2325.  
14580341 C.S.Hayes, and R.T.Sauer (2003).
Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control.
  Mol Cell, 12, 903-911.  
12904796 S.Gutmann, P.W.Haebel, L.Metzinger, M.Sutter, B.Felden, and N.Ban (2003).
Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB.
  Nature, 424, 699-703.
PDB code: 1p6v
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.