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PDBsum entry 1qzc
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protein dna_rna links
RNA binding protein/RNA PDB id
1qzc
Contents
Protein chain
124 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
1qzc
Name: RNA binding protein/RNA
Title: Coordinates of s12, sh44, lh69 and srl separately fitted into the cryo-em map of ef-tu ternary complex (gdp.Kirromycin) bound 70s ribosome
Structure: 16s rrna. Chain: a. Fragment: helix 44. 23s rrna. Chain: b. Fragment: helix 69. 23s rrna. Chain: c. Fragment: sarcin/ricin loop (srl).
Source: Escherichia coli. Organism_taxid: 562. Strain: mre 600. Thermus thermophilus. Organism_taxid: 274
Authors: M.Valle,A.Zavialov,W.Li,S.M.Stagg,J.Sengupta,R.C.Nielsen,P.Nissen, S.C.Harvey,M.Ehrenberg,J.Frank
Key ref:
M.Valle et al. (2003). Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat Struct Biol, 10, 899-906. PubMed id: 14566331 DOI: 10.1038/nsb1003
Date:
16-Sep-03     Release date:   04-Nov-03    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		132 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure

DNA/RNA chains
  C-G-C-C-C-G-U-C-A-C-G-C-C-A-U-G-G-G-A-G-C-G-U-G-A-C-U-G-G-G-G-C-G-A-A-G-U-C-G- 44 bases
  G-G-C-C-G-U-A-A-C-U-A-U-A-A-C-G-G-U-C-C 20 bases
  G-A-C-C-G-U-A-U-A-G-U-A-C-G-A-G-A-G-G-A-A-C-U-A-C-G-G 27 bases

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1038/nsb1003 Nat Struct Biol 10:899-906 (2003)
PubMed id: 14566331  
 
 
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy.
M.Valle, A.Zavialov, W.Li, S.M.Stagg, J.Sengupta, R.C.Nielsen, P.Nissen, S.C.Harvey, M.Ehrenberg, J.Frank.
 
  ABSTRACT  
 
Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, at a resolution of approximately 9 A, showing that during the incorporation of the aa-tRNA into the 70S ribosome of Escherichia coli, the flexibility of aa-tRNA allows the initial codon recognition and its accommodation into the ribosomal A site. In addition, a conformational change observed in the GTPase-associated center (GAC) of the ribosomal 50S subunit may provide the mechanism by which the ribosome promotes a relative movement of the aa-tRNA with respect to EF-Tu. This relative rearrangement seems to facilitate codon recognition by the incoming aa-tRNA, and to provide the codon-anticodon recognition-dependent signal for the GTPase activity of EF-Tu. From these new findings we propose a mechanism that can explain the sequence of events during the decoding of mRNA on the ribosome.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Topology of the decoding site. (a) 30S subunit portion isolated from the 70S -fMet-tRNA^fMet -Phe-tRNA^Phe -EF-Tu -GDP -kir complex, seen from the intersubunit space. The architecture of the decoding site (dc) shows a density in the region of the A-site codon (labeled with an asterisk) and a low-density region (indicated by an arrow) within SH44. (b) Ribbons representation of the docked atomic coordinates for SH44, ribosomal protein S12 (S12), SH18 and the A site codon (cd) from Ogle and co-workers21 within the density region extracted from a. 		Figure 6.
Figure 6. Coupling of the conformational change of the GAC with the movement of aa-tRNA. (a) Comparison of the aa-tRNA position defined inside the cryo-EM density for the ternary complex (green) versus the position of the aa-tRNA in the atomic coordinates of Phe-tRNA^Phe -EF-Tu -GDPNP -kir (gray). The ribbons representation of the GAC and the SRL serves as a frame of reference to make it apparent that the change in the aa-tRNA position follows the conformational change of the GAC while the aa-tRNA maintains its position in the region of the SRL. The GAC position shown correspond to the fitting of the atomic coordinates in the 'closed' GAC from the 70S -fMet-tRNA^fMet -Phe-tRNA^Phe -EF-Tu -GDP -kir complex. The ribosomal orientation is depicted in the thumbnail. (b -d) The postulated coupling between the movement of the GAC and the approach of the aa-tRNA to LH69. In a hypothetical initial binding, the 'open' GAC would interact with the aa-tRNA delivered in the ternary complex by EF-Tu (b). The transition of the GAC to the closed conformation (c) brings the aa-tRNA in contact with LH69. The aa-tRNA -LH69 interaction facilitates a distortion in the aa-tRNA (d) that reorients the anticodon arm (in the region encircled) and allows a codon (cd)-anticodon recognition.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 899-906) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21549313 C.Chen, B.Stevens, J.Kaur, D.Cabral, H.Liu, Y.Wang, H.Zhang, G.Rosenblum, Z.Smilansky, Y.E.Goldman, and B.S.Cooperman (2011).
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Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
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21365677 W.Li, L.G.Trabuco, K.Schulten, and J.Frank (2011).
Molecular dynamics of EF-G during translocation.
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PDB code: 3izp
21378755 X.Agirrezabala, E.Schreiner, L.G.Trabuco, J.Lei, R.F.Ortiz-Meoz, K.Schulten, R.Green, and J.Frank (2011).
Structural insights into cognate versus near-cognate discrimination during decoding.
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PDB codes: 3izt 3izu 3izv 3izw
21368154 Z.Guo, M.Gibson, S.Sitha, S.Chu, and U.Mohanty (2011).
Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome.
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20348921 N.Clementi, A.Chirkova, B.Puffer, R.Micura, and N.Polacek (2010).
Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation.
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Functional interactions by transfer RNAs in the ribosome.
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A role for the 30S subunit E site in maintenance of the translational reading frame.
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20004164 A.Matsumoto, and H.Ishida (2009).
Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures.
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The ribosome as a conveying thermal ratchet machine.
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19213046 D.M.Hamburg, M.J.Suh, and P.A.Limbach (2009).
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19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
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19122150 E.Villa, J.Sengupta, L.G.Trabuco, J.LeBarron, W.T.Baxter, T.R.Shaikh, R.A.Grassucci, P.Nissen, M.Ehrenberg, K.Schulten, and J.Frank (2009).
Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.
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PDB codes: 3fih 3fik
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.
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19239893 H.S.Zaher, and R.Green (2009).
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GTPase activation of elongation factor EF-Tu by the ribosome during decoding.
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PDB codes: 3fic 3fin
19497863 M.R.Sharma, T.M.Booth, L.Simpson, D.A.Maslov, and R.K.Agrawal (2009).
Structure of a mitochondrial ribosome with minimal RNA.
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PDB codes: 3iy8 3iy9
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Ribosomal translocation: one step closer to the molecular mechanism.
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19095621 S.T.Gregory, J.F.Carr, and A.E.Dahlberg (2009).
A signal relay between ribosomal protein S12 and elongation factor EF-Tu during decoding of mRNA.
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19129224 T.Dale, R.P.Fahlman, M.Olejniczak, and O.C.Uhlenbeck (2009).
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20025795 X.Agirrezabala, and J.Frank (2009).
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Perturbation of the tRNA tertiary core differentially affects specific steps of the elongation cycle.
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PDB codes: 2zjp 2zjq 2zjr 3cf5
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PDB codes: 3dny 3dwu
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Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
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Protein structure fitting and refinement guided by cryo-EM density.
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PDB codes: 2zkq 2zkr
18552770 P.F.Agris (2008).
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Visualization of macromolecular complexes using cryo-electron microscopy with FEI Tecnai transmission electron microscopes.
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18518820 R.A.Marshall, C.E.Aitken, M.Dorywalska, and J.D.Puglisi (2008).
Translation at the single-molecule level.
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18572416 R.K.Tan, B.Devkota, and S.C.Harvey (2008).
YUP.SCX: coaxing atomic models into medium resolution electron density maps.
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18614050 S.Ledoux, and O.C.Uhlenbeck (2008).
Different aa-tRNAs are selected uniformly on the ribosome.
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19172743 S.R.Connell, M.Topf, Y.Qin, D.N.Wilson, T.Mielke, P.Fucini, K.H.Nierhaus, and C.M.Spahn (2008).
A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
  Nat Struct Mol Biol, 15, 910-915.
PDB codes: 3deg 3qkf 3r4e
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
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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.
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18632761 T.V.Budkevich, A.V.El'skaya, and K.H.Nierhaus (2008).
Features of 80S mammalian ribosome and its subunits.
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19020518 W.Li, X.Agirrezabala, J.Lei, L.Bouakaz, J.L.Brunelle, R.F.Ortiz-Meoz, R.Green, S.Sanyal, M.Ehrenberg, and J.Frank (2008).
Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
  EMBO J, 27, 3322-3331.
PDB codes: 3ep2 3eq3 3eq4
18951087 X.Agirrezabala, J.Lei, J.L.Brunelle, R.F.Ortiz-Meoz, R.Green, and J.Frank (2008).
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome.
  Mol Cell, 32, 190-197.  
17897673 A.Korostelev, and H.F.Noller (2007).
Analysis of structural dynamics in the ribosome by TLS crystallographic refinement.
  J Mol Biol, 373, 1058-1070.  
17369838 A.L.Konevega, N.Fischer, Y.P.Semenkov, H.Stark, W.Wintermeyer, and M.V.Rodnina (2007).
Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.
  Nat Struct Mol Biol, 14, 318-324.  
17446867 D.J.Taylor, J.Nilsson, A.R.Merrill, G.R.Andersen, P.Nissen, and J.Frank (2007).
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
  EMBO J, 26, 2421-2431.
PDB codes: 2p8w 2p8x 2p8y 2p8z
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
17317624 J.B.Munro, R.B.Altman, N.O'Connor, and S.C.Blanchard (2007).
Identification of two distinct hybrid state intermediates on the ribosome.
  Mol Cell, 25, 505-517.  
18003906 J.Frank, H.Gao, J.Sengupta, N.Gao, and D.J.Taylor (2007).
The process of mRNA-tRNA translocation.
  Proc Natl Acad Sci U S A, 104, 19671-19678.  
17159993 L.Cochella, J.L.Brunelle, and R.Green (2007).
Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome.
  Nat Struct Mol Biol, 14, 30-36.  
17328911 L.E.Sanderson, and O.C.Uhlenbeck (2007).
Directed mutagenesis identifies amino acid residues involved in elongation factor Tu binding to yeast Phe-tRNAPhe.
  J Mol Biol, 368, 119-130.  
17685395 M.A.Ditzler, E.A.Alemán, D.Rueda, and N.G.Walter (2007).
Focus on function: single molecule RNA enzymology.
  Biopolymers, 87, 302-316.  
17379816 M.E.Saks, and J.S.Conery (2007).
Anticodon-dependent conservation of bacterial tRNA gene sequences.
  RNA, 13, 651-660.  
18079724 R.A.Grassucci, D.J.Taylor, and J.Frank (2007).
Preparation of macromolecular complexes for cryo-electron microscopy.
  Nat Protoc, 2, 3239-3246.  
17951333 R.L.Gonzalez, S.Chu, and J.D.Puglisi (2007).
Thiostrepton inhibition of tRNA delivery to the ribosome.
  RNA, 13, 2091-2097.  
17652139 R.Oliva, A.Tramontano, and L.Cavallo (2007).
Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs.
  RNA, 13, 1427-1436.  
17349960 S.R.Connell, C.Takemoto, D.N.Wilson, H.Wang, K.Murayama, T.Terada, M.Shirouzu, M.Rost, M.Schüler, J.Giesebrecht, M.Dabrowski, T.Mielke, P.Fucini, S.Yokoyama, and C.M.Spahn (2007).
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
  Mol Cell, 25, 751-764.
PDB code: 2om7
17925437 W.Li, and J.Frank (2007).
Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data.
  Proc Natl Acad Sci U S A, 104, 16540-16545.  
16979906 X.Yan, K.A.Dryden, J.Tang, and T.S.Baker (2007).
Ab initio random model method facilitates 3D reconstruction of icosahedral particles.
  J Struct Biol, 157, 211-225.  
16962654 A.Korostelev, S.Trakhanov, M.Laurberg, and H.F.Noller (2006).
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
  Cell, 126, 1065-1077.
PDB codes: 1vsa 2ow8
16855312 A.Liljas (2006).
On the complementarity of methods in structural biology.
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16716074 C.Maeder, G.L.Conn, and D.E.Draper (2006).
Optimization of a ribosomal structural domain by natural selection.
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16943448 F.Tama, G.Ren, C.L.Brooks, and A.K.Mitra (2006).
Model of the toxic complex of anthrax: responsive conformational changes in both the lethal factor and the protective antigen heptamer.
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16973438 I.K.Ali, L.Lancaster, J.Feinberg, S.Joseph, and H.F.Noller (2006).
Deletion of a conserved, central ribosomal intersubunit RNA bridge.
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16713583 K.Mitra, C.Schaffitzel, F.Fabiola, M.S.Chapman, N.Ban, and J.Frank (2006).
Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
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PDB codes: 2gy9 2gya 2gyb 2gyc
16689638 K.Mitra, and J.Frank (2006).
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.
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16890441 K.P.Hofmann, C.M.Spahn, R.Heinrich, and U.Heinemann (2006).
Building functional modules from molecular interactions.
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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
16621804 N.Hirabayashi, N.S.Sato, and T.Suzuki (2006).
Conserved loop sequence of helix 69 in Escherichia coli 23 S rRNA is involved in A-site tRNA binding and translational fidelity.
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Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.
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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
16601123 Y.Shimizu, and T.Ueda (2006).
SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans-translation initiation.
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Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis.
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15985150 A.V.Zavialov, V.V.Hauryliuk, and M.Ehrenberg (2005).
Guanine-nucleotide exchange on ribosome-bound elongation factor G initiates the translocation of tRNAs.
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16272117 B.S.Schuwirth, M.A.Borovinskaya, C.W.Hau, W.Zhang, A.Vila-Sanjurjo, J.M.Holton, and J.H.Cate (2005).
Structures of the bacterial ribosome at 3.5 A resolution.
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PDB codes: 2avy 2aw4 2aw7 2awb
16314459 C.L.Shenvi, K.C.Dong, E.M.Friedman, J.A.Hanson, and J.H.Cate (2005).
Accessibility of 18S rRNA in human 40S subunits and 80S ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics.
  RNA, 11, 1898-1908.  
15985151 C.S.Fraser, and J.W.Hershey (2005).
Movement in ribosome translocation.
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15853795 D.E.Brodersen, and P.Nissen (2005).
The social life of ribosomal proteins.
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15722438 F.Rázga, J.Koca, J.Sponer, and N.B.Leontis (2005).
Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.
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15766541 H.Gao, and J.Frank (2005).
Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement.
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15952884 J.M.Ogle, and V.Ramakrishnan (2005).
Structural insights into translational fidelity.
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15922593 J.Nilsson, and P.Nissen (2005).
Elongation factors on the ribosome.
  Curr Opin Struct Biol, 15, 349-354.  
16261170 J.Poehlsgaard, and S.Douthwaite (2005).
The bacterial ribosome as a target for antibiotics.
  Nat Rev Microbiol, 3, 870-881.  
16249344 K.Y.Sanbonmatsu, S.Joseph, and C.S.Tung (2005).
Simulating movement of tRNA into the ribosome during decoding.
  Proc Natl Acad Sci U S A, 102, 15854-15859.  
15905403 L.Cochella, and R.Green (2005).
An active role for tRNA in decoding beyond codon:anticodon pairing.
  Science, 308, 1178-1180.  
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
15616587 M.Leibundgut, C.Frick, M.Thanbichler, A.Böck, and N.Ban (2005).
Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors.
  EMBO J, 24, 11-22.
PDB codes: 1wb1 1wb2 1wb3 4ac9 4aca 4acb
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
16244128 T.Dale, and O.C.Uhlenbeck (2005).
Binding of misacylated tRNAs to the ribosomal A site.
  RNA, 11, 1610-1615.  
15905389 T.Daviter, F.V.Murphy, and V.Ramakrishnan (2005).
Molecular biology. A renewed focus on transfer RNA.
  Science, 308, 1123-1124.  
16140524 W.Jiang, and S.J.Ludtke (2005).
Electron cryomicroscopy of single particles at subnanometer resolution.
  Curr Opin Struct Biol, 15, 571-577.  
15487937 A.Yonath, and A.Bashan (2004).
Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
  Annu Rev Microbiol, 58, 233-251.  
14976550 C.M.Spahn, M.G.Gomez-Lorenzo, R.A.Grassucci, R.Jørgensen, G.R.Andersen, R.Beckmann, P.A.Penczek, J.P.Ballesta, and J.Frank (2004).
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
  EMBO J, 23, 1008-1019.
PDB codes: 1s1h 1s1i
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.  
15004548 K.B.Gromadski, and M.V.Rodnina (2004).
Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome.
  Nat Struct Mol Biol, 11, 316-322.  
15247429 M.Léger, S.Sidani, and L.Brakier-Gingras (2004).
A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1.
  RNA, 10, 1225-1235.  
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
15448679 S.C.Blanchard, R.L.Gonzalez, H.D.Kim, S.Chu, and J.D.Puglisi (2004).
tRNA selection and kinetic proofreading in translation.
  Nat Struct Mol Biol, 11, 1008-1014.  
15139808 S.Subramaniam, and J.L.Milne (2004).
Three-dimensional electron microscopy at molecular resolution.
  Annu Rev Biophys Biomol Struct, 33, 141-155.  
15469618 Y.Yap, X.Zhang, M.T.Ling, X.Wang, Y.C.Wong, and A.Danchin (2004).
Classification between normal and tumor tissues based on the pair-wise gene expression ratio.
  BMC Cancer, 4, 72.  
14659007 J.Frank (2003).
Toward an understanding of the structural basis of translation.
  Genome Biol, 4, 237.  
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.

 

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