spacer
spacer

PDBsum entry 1jqm

Go to PDB code: 
links
Ribosome PDB id
1jqm
Jmol
Contents
PDB id:
1jqm
Name: Ribosome
Title: Fitting of l11 protein and elongation factor g (ef-g) in the cryo-em map of e. Coli 70s ribosome bound with ef-g, gdp and fusidic acid
Structure: 50s ribosomal protein l11. Chain: a. Other_details: l11 from e. Coli 70s ribosome modeled by crystal structure of l11 from thermatogoma maritima. Elongation factor g. Chain: b. Synonym: ef-g. Translation elongation factor ef-g. Other_details: ef-g from e. Coli 70s ribosome modeled by crystal structure of ef-g from thermus thermophilus
Source: Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
Authors: R.K.Agrawal,J.Linde,J.Segupta,K.H.Nierhaus,J.Frank
Key ref:
R.K.Agrawal et al. (2001). Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation. J Mol Biol, 311, 777-787. PubMed id: 11518530 DOI: 10.1006/jmbi.2001.4907
Date:
07-Aug-01     Release date:   07-Sep-01    
 Headers
 References
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   3 terms 
  Biochemical function     structural constituent of ribosome     8 terms  

 

 
DOI no: 10.1006/jmbi.2001.4907 J Mol Biol 311:777-787 (2001)
PubMed id: 11518530  
 
 
Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation.
R.K.Agrawal, J.Linde, J.Sengupta, K.H.Nierhaus, J.Frank.
 
  ABSTRACT  
 
L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the 50 S subunit failed to locate the N-terminal domain of the protein. We have determined the position of the complete L11 protein by comparing a three-dimensional cryo-EM reconstruction of the 70 S ribosome, isolated from a mutant lacking ribosomal protein L11, with the three-dimensional map of the wild-type ribosome. Fitting of the X-ray coordinates of L11-23 S RNA complex and EF-G into the cryo-EM maps combined with molecular modeling, reveals that, following EF-G-dependent GTP hydrolysis, domain V of EF-G intrudes into the cleft between the 23 S ribosomal RNA and the N-terminal domain of L11 (where the antibiotic thiostrepton binds), causing the N-terminal domain to move and thereby inducing the formation of the arc-like connection with the G' domain of EF-G. The results provide a new insight into the mechanism of EF-G-dependent translocation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereo-view comparison of the cryo-EM structures of L11-depleted 70 S ribosome and wild-type (control) ribosome. (a) L11-depleted ribosome and (b) control ribosome.[33] The ribosome maps are shown from the 30 S subunit side. Arrows in (a) point to the absence of density in the stalk-base (Sb) region, while in (b) they point to the additional density in the control. Landmarks of the 50 S subunit: L1, protein L1; St, stalk; Sb, stalk base. Landmarks of the 30 S subunit: h, head; b, body; and sp, spur.
Figure 2.
Figure 2. Stereo-view representation of the fitting of the X-ray structure of L11 into the corresponding cryo-EM density. The stalk-base regions of cryo-EM densities of control (grey) and L11-depleted (blue) 70 S ribosomes are shown as wire-mesh structures. (a) Results of fitting the X-ray structure of the complete L11-58 nt RNA complex[22] as one rigid body (see Gabashvili et al.[28]). The RNA portion is not shown. (b) The optimum fit obtained for the NTD (N, yellow) by rotating it around a pivoting point between the two proline residues, 73 and 74, of the linker between the CTD (C, green) and NTD.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 311, 777-787) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22407015 L.Wang, F.Yang, D.Zhang, Z.Chen, R.M.Xu, K.H.Nierhaus, W.Gong, and Y.Qin (2012).
A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.
  Nat Struct Mol Biol, 19, 403-410.  
21428957 M.V.Rodnina, and W.Wintermeyer (2011).
The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation.
  Biochem Soc Trans, 39, 658-662.  
20718859 Y.Chen, R.K.Koripella, S.Sanyal, and M.Selmer (2010).
Staphylococcus aureus elongation factor G--structure and analysis of a target for fusidic acid.
  FEBS J, 277, 3789-3803.
PDB code: 2xex
19822758 A.Korostelev, M.Laurberg, and H.F.Noller (2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
  Proc Natl Acad Sci U S A, 106, 18195-18200.  
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
19366171 H.Qin, C.Grigoriadou, and B.S.Cooperman (2009).
Interaction of IF2 with the ribosomal GTPase-associated center during 70S initiation complex formation.
  Biochemistry, 48, 4699-4706.  
19722627 J.Wang, X.Zuo, P.Yu, I.J.Byeon, J.Jung, X.Wang, M.Dyba, S.Seifert, C.D.Schwieters, J.Qin, A.M.Gronenborn, and Y.X.Wang (2009).
Determination of multicomponent protein structures in solution using global orientation and shape restraints.
  J Am Chem Soc, 131, 10507-10515.
PDB codes: 2klj 2klk 2klm
19686666 O.Kurkcuoglu, O.T.Turgut, S.Cansu, R.L.Jernigan, and P.Doruker (2009).
Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.
  Biophys J, 97, 1178-1187.  
18832371 A.Meskauskas, and J.D.Dinman (2008).
Ribosomal protein L3 functions as a 'rocker switch' to aid in coordinating of large subunit-associated functions in eukaryotes and Archaea.
  Nucleic Acids Res, 36, 6175-6186.  
18755834 L.Lancaster, N.J.Lambert, E.J.Maklan, L.H.Horan, and H.F.Noller (2008).
The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit.
  RNA, 14, 1999-2012.  
19029596 O.Kurkcuoglu, P.Doruker, T.Z.Sen, A.Kloczkowski, and R.L.Jernigan (2008).
The ribosome structure controls and directs mRNA entry, translocation and exit dynamics.
  Phys Biol, 5, 046005.  
18252772 T.Miyoshi, and T.Uchiumi (2008).
Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes.
  Nucleic Acids Res, 36, 1783-1791.  
17940088 A.García-Marcos, A.Morreale, E.Guarinos, E.Briones, M.Remacha, A.R.Ortiz, and J.P.Ballesta (2007).
In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton.
  Nucleic Acids Res, 35, 7109-7117.  
17610498 B.Polevoda, and F.Sherman (2007).
Methylation of proteins involved in translation.
  Mol Microbiol, 65, 590-606.  
17292917 D.Lee, J.D.Walsh, P.Yu, M.A.Markus, T.Choli-Papadopoulou, C.D.Schwieters, S.Krueger, D.E.Draper, and Y.X.Wang (2007).
The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.
  J Mol Biol, 367, 1007-1022.
PDB codes: 2e34 2e35 2e36 2h8w
17317625 D.Pan, S.V.Kirillov, and B.S.Cooperman (2007).
Kinetically competent intermediates in the translocation step of protein synthesis.
  Mol Cell, 25, 519-529.  
17315147 D.Shcherbakov, and W.Piendl (2007).
A novel view of gel-shifts: analysis of RNA-protein complexes using a two-color fluorescence dye procedure.
  Electrophoresis, 28, 749-755.  
17553840 F.Rázga, J.Koca, A.Mokdad, and J.Sponer (2007).
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.
  Nucleic Acids Res, 35, 4007-4017.  
17215866 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2007).
Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA.
  EMBO J, 26, 567-577.
PDB codes: 2nxc 2nxe 2nxj 2nxn
17540173 H.Gao, Z.Zhou, U.Rawat, C.Huang, L.Bouakaz, C.Wang, Z.Cheng, Y.Liu, A.Zavialov, R.Gursky, S.Sanyal, M.Ehrenberg, J.Frank, and H.Song (2007).
RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors.
  Cell, 129, 929-941.
PDB codes: 2h5e 2o0f
17169991 H.R.Jonker, S.Ilin, S.K.Grimm, J.Wöhnert, and H.Schwalbe (2007).
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
  Nucleic Acids Res, 35, 441-454.
PDB codes: 2jq7 2nyo
17082187 R.Søe, R.T.Mosley, M.Justice, J.Nielsen-Kahn, M.Shastry, A.R.Merrill, and G.R.Andersen (2007).
Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2.
  J Biol Chem, 282, 657-666.
PDB codes: 2e1r 2npf
17923494 T.Norström, J.Lannergård, and D.Hughes (2007).
Genetic and phenotypic identification of fusidic acid-resistant mutants with the small-colony-variant phenotype in Staphylococcus aureus.
  Antimicrob Agents Chemother, 51, 4438-4446.  
16716074 C.Maeder, G.L.Conn, and D.E.Draper (2006).
Optimization of a ribosomal structural domain by natural selection.
  Biochemistry, 45, 6635-6643.  
16371360 L.Bouakaz, E.Bouakaz, E.J.Murgola, M.Ehrenberg, and S.Sanyal (2006).
The role of ribosomal protein L11 in class I release factor-mediated translation termination and translational accuracy.
  J Biol Chem, 281, 4548-4556.  
16682558 W.Li, J.Sengupta, B.K.Rath, and J.Frank (2006).
Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations.
  RNA, 12, 1240-1253.
PDB code: 2gkz
16188884 A.Hagiya, T.Naganuma, Y.Maki, J.Ohta, Y.Tohkairin, T.Shimizu, T.Nomura, A.Hachimori, and T.Uchiumi (2005).
A mode of assembly of P0, P1, and P2 proteins at the GTPase-associated center in animal ribosome: in vitro analyses with P0 truncation mutants.
  J Biol Chem, 280, 39193-39199.  
15985151 C.S.Fraser, and J.W.Hershey (2005).
Movement in ribosome translocation.
  J Biol, 4, 8.  
15951386 J.Trylska, V.Tozzini, and J.A.McCammon (2005).
Exploring global motions and correlations in the ribosome.
  Biophys J, 89, 1455-1463.  
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
15989950 M.Diaconu, U.Kothe, F.Schlünzen, N.Fischer, J.M.Harms, A.G.Tonevitsky, H.Stark, M.V.Rodnina, and M.C.Wahl (2005).
Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
  Cell, 121, 991.
PDB codes: 1zav 1zaw 1zax 1zb4
16337596 P.P.Datta, M.R.Sharma, L.Qi, J.Frank, and R.K.Agrawal (2005).
Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM.
  Mol Cell, 20, 723-731.
PDB code: 2bcw
16014631 P.V.Sergiev, D.V.Lesnyak, D.E.Burakovsky, S.V.Kiparisov, A.A.Leonov, A.A.Bogdanov, R.Brimacombe, and O.A.Dontsova (2005).
Alteration in location of a conserved GTPase-associated center of the ribosome induced by mutagenesis influences the structure of peptidyltransferase center and activity of elongation factor G.
  J Biol Chem, 280, 31882-31889.  
16094695 S.Ilin, A.Hoskins, O.Ohlenschläger, H.R.Jonker, H.Schwalbe, and J.Wöhnert (2005).
Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima.
  Chembiochem, 6, 1611-1618.
PDB code: 2k3f
15972821 S.L.Bausch, E.Poliakova, and D.E.Draper (2005).
Interactions of the N-terminal domain of ribosomal protein L11 with thiostrepton and rRNA.
  J Biol Chem, 280, 29956-29963.  
16377566 S.Petry, D.E.Brodersen, F.V.Murphy, C.M.Dunham, M.Selmer, M.J.Tarry, A.C.Kelley, and V.Ramakrishnan (2005).
Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon.
  Cell, 123, 1255-1266.
PDB codes: 2b64 2b66 2b9m 2b9n 2b9o 2b9p
15661844 V.S.Raj, H.Kaji, and A.Kaji (2005).
Interaction of RRF and EF-G from E. coli and T. thermophilus with ribosomes from both origins--insight into the mechanism of the ribosome recycling step.
  RNA, 11, 275-284.  
15492007 W.S.Bowen, N.Van Dyke, E.J.Murgola, J.S.Lodmell, and W.E.Hill (2005).
Interaction of thiostrepton and elongation factor-G with the ribosomal protein L11-binding domain.
  J Biol Chem, 280, 2934-2943.  
15199170 D.M.Cameron, J.Thompson, S.T.Gregory, P.E.March, and A.E.Dahlberg (2004).
Thiostrepton-resistant mutants of Thermus thermophilus.
  Nucleic Acids Res, 32, 3220-3227.  
15317787 D.M.Cameron, S.T.Gregory, J.Thompson, M.J.Suh, P.A.Limbach, and A.E.Dahlberg (2004).
Thermus thermophilus L11 methyltransferase, PrmA, is dispensable for growth and preferentially modifies free ribosomal protein L11 prior to ribosome assembly.
  J Bacteriol, 186, 5819-5825.  
15103642 F.Park, K.Gajiwala, G.Eroshkina, E.Furlong, D.He, Y.Batiyenko, R.Romero, J.Christopher, J.Badger, J.Hendle, J.Lin, T.Peat, and S.Buchanan (2004).
Crystal structure of YIGZ, a conserved hypothetical protein from Escherichia coli k12 with a novel fold.
  Proteins, 55, 775-777.
PDB code: 1vi7
15274086 J.Trylska, R.Konecny, F.Tama, C.L.Brooks, and J.A.McCammon (2004).
Ribosome motions modulate electrostatic properties.
  Biopolymers, 74, 423-431.  
15178758 R.K.Agrawal, M.R.Sharma, M.C.Kiel, G.Hirokawa, T.M.Booth, C.M.Spahn, R.A.Grassucci, A.Kaji, and J.Frank (2004).
Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications.
  Proc Natl Acad Sci U S A, 101, 8900-8905.
PDB codes: 1t1m 1t1o
12809609 H.Gao, J.Sengupta, M.Valle, A.Korostelev, N.Eswar, S.M.Stagg, P.Van Roey, R.K.Agrawal, S.C.Harvey, A.Sali, M.S.Chapman, and J.Frank (2003).
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
  Cell, 113, 789-801.
PDB codes: 1p6g 1p85 1p86 1p87
12548625 J.Frank (2003).
Electron microscopy of functional ribosome complexes.
  Biopolymers, 68, 223-233.  
12960150 M.C.Kiel, V.S.Raj, H.Kaji, and A.Kaji (2003).
Release of ribosome-bound ribosome recycling factor by elongation factor G.
  J Biol Chem, 278, 48041-48050.  
12093756 M.Valle, J.Sengupta, N.K.Swami, R.A.Grassucci, N.Burkhardt, K.H.Nierhaus, R.K.Agrawal, and J.Frank (2002).
Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.
  EMBO J, 21, 3557-3567.
PDB codes: 1ls2 1lu3
12198134 T.Uchiumi, S.Honma, Y.Endo, and A.Hachimori (2002).
Ribosomal proteins at the stalk region modulate functional rRNA structures in the GTPase center.
  J Biol Chem, 277, 41401-41409.  
12762009 J.Frank, and R.K.Agrawal (2001).
Ratchet-like movements between the two ribosomal subunits: their implications in elongation factor recognition and tRNA translocation.
  Cold Spring Harb Symp Quant Biol, 66, 67-75.  
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.