PDBsum entry 1pn7

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protein dna_rna links
RNA binding protein/RNA PDB id
Protein chains
124 a.a.* *
133 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
Name: RNA binding protein/RNA
Title: Coordinates of s12, l11 proteins and p-tRNA, from the 70s x- ray structure aligned to the 70s cryo-em map of e.Coli ribosome
Structure: P-tRNA. Chain: c. Engineered: yes. 30s ribosomal protein s12. Chain: o. 50s ribosomal protein l11. Chain: l
Source: Synthetic: yes. Thermus thermophilus. Organism_taxid: 274. Thermotoga maritima. Organism_taxid: 2336
Authors: M.Valle,A.Zavialov,J.Sengupta,U.Rawat,M.Ehrenberg,J.Frank
Key ref:
M.Valle et al. (2003). Locking and unlocking of ribosomal motions. Cell, 114, 123-134. PubMed id: 12859903 DOI: 10.1016/S0092-8674(03)00476-8
12-Jun-03     Release date:   15-Jul-03    

Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P29395  (RL11_THEMA) -  50S ribosomal protein L11
141 a.a.
133 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     5 terms  


    Added reference    
DOI no: 10.1016/S0092-8674(03)00476-8 Cell 114:123-134 (2003)
PubMed id: 12859903  
Locking and unlocking of ribosomal motions.
M.Valle, A.Zavialov, J.Sengupta, U.Rawat, M.Ehrenberg, J.Frank.
During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the direction of the mRNA movement. By means of cryo-electron microscopy we observe that this rotation is accompanied by a 20 A movement of the L1 stalk of the 50S subunit, implying that this region is involved in the translocation of deacylated tRNAs from the P to the E site. These ribosomal motions can occur only when the P-site tRNA is deacylated. Prior to peptidyl-transfer to the A-site tRNA or peptide removal, the presence of the charged P-site tRNA locks the ribosome and prohibits both of these motions.
  Selected figure(s)  
Figure 4.
Figure 4. Docking of EF-GStereo views of the fitted EF-G·GDP structure in the cryo-EM density for EF-G·GDPNP (semitransparent red). In (A) relative movements between domains were allowed, while in (B) the EF-G·GDP coordinates were used as a rigid body and only domains I and II were docked.
Figure 5.
Figure 5. A Pretranslocational ComplexRendering of the cryo-EM map for 70S ribosome bearing deacylated tRNA^fMet in the P site (green) and dipeptidyl fMet-Phe-tRNA^Phe in the A site (magenta). The E site is occupied by deacylated tRNA (orange) available in the solution.(A) shows the segmented map in solid, while in (B) a semitransparent representation of the ribosomal subunits allows the visualization of the tRNAs in A, P, and E sites.
  The above figures are reprinted by permission from Cell Press: Cell (2003, 114, 123-134) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22337051 E.A.Dethoff, J.Chugh, A.M.Mustoe, and H.M.Al-Hashimi (2012).
Functional complexity and regulation through RNA dynamics.
  Nature, 482, 322-330.  
22902368 L.Wang, A.Pulk, M.R.Wasserman, M.B.Feldman, R.B.Altman, J.H.Doudna Cate, and S.C.Blanchard (2012).
Allosteric control of the ribosome by small-molecule antibiotics.
  Nat Struct Mol Biol, 19, 957-963.
PDB codes: 4gaq 4gar 4gas 4gau
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.  
22751017 S.Lebaron, C.Schneider, R.W.van Nues, A.Swiatkowska, D.Walsh, B.Böttcher, S.Granneman, N.J.Watkins, and D.Tollervey (2012).
Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits.
  Nat Struct Mol Biol, 19, 744-753.  
21263169 A.K.Sharma, and D.Chowdhury (2011).
Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding.
  Phys Biol, 8, 026005.  
21256733 A.Petrov, G.Kornberg, S.O'Leary, A.Tsai, S.Uemura, and J.D.Puglisi (2011).
Dynamics of the translational machinery.
  Curr Opin Struct Biol, 21, 137-145.  
21539788 C.Y.Liu, M.T.Qureshi, and T.H.Lee (2011).
Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
  Biophys J, 100, 2201-2208.  
21399643 D.N.Ermolenko, and H.F.Noller (2011).
mRNA translocation occurs during the second step of ribosomal intersubunit rotation.
  Nat Struct Mol Biol, 18, 457-462.  
21857664 J.Fei, A.C.Richard, J.E.Bronson, and R.L.Gonzalez (2011).
Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis.
  Nat Struct Mol Biol, 18, 1043-1051.  
21383139 J.Fu, J.B.Munro, S.C.Blanchard, and J.Frank (2011).
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
  Proc Natl Acad Sci U S A, 108, 4817-4821.  
21152913 K.Kulczycka, M.Długosz, and J.Trylska (2011).
Molecular dynamics of ribosomal elongation factors G and Tu.
  Eur Biophys J, 40, 289-303.  
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.  
21336521 M.Valle (2011).
Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome.
  Eur Biophys J, 40, 589-597.  
21365677 W.Li, L.G.Trabuco, K.Schulten, and J.Frank (2011).
Molecular dynamics of EF-G during translocation.
  Proteins, 79, 1478-1486.
PDB code: 3izp
21734708 X.Qu, J.D.Wen, L.Lancaster, H.F.Noller, C.Bustamante, and I.Tinoco (2011).
The ribosome uses two active mechanisms to unwind messenger RNA during translation.
  Nature, 475, 118-121.  
21109664 A.Ben-Shem, L.Jenner, G.Yusupova, and M.Yusupov (2010).
Crystal structure of the eukaryotic ribosome.
  Science, 330, 1203-1209.
PDB codes: 3o2z 3o30 3o58 3o5h
21124459 A.H.Ratje, J.Loerke, A.Mikolajka, M.Brünner, P.W.Hildebrand, A.L.Starosta, A.Dönhöfer, S.R.Connell, P.Fucini, T.Mielke, P.C.Whitford, J.N.Onuchic, Y.Yu, K.Y.Sanbonmatsu, R.K.Hartmann, P.A.Penczek, D.N.Wilson, and C.M.Spahn (2010).
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
  Nature, 468, 713-716.
PDB codes: 2xsy 2xtg 2xux 2xuy
20192783 C.E.Aitken, A.Petrov, and J.D.Puglisi (2010).
Single ribosome dynamics and the mechanism of translation.
  Annu Rev Biophys, 39, 491-513.  
20562856 C.E.Aitken, and J.D.Puglisi (2010).
Following the intersubunit conformation of the ribosome during translation in real time.
  Nat Struct Mol Biol, 17, 793-800.  
20423979 C.J.Jang, and E.Jan (2010).
Modular domains of the Dicistroviridae intergenic internal ribosome entry site.
  RNA, 16, 1182-1195.  
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
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
21057527 J.B.Munro, M.R.Wasserman, R.B.Altman, L.Wang, and S.C.Blanchard (2010).
Correlated conformational events in EF-G and the ribosome regulate translocation.
  Nat Struct Mol Biol, 17, 1470-1477.  
20018653 J.B.Munro, R.B.Altman, C.S.Tung, J.H.Cate, K.Y.Sanbonmatsu, and S.C.Blanchard (2010).
Spontaneous formation of the unlocked state of the ribosome is a multistep process.
  Proc Natl Acad Sci U S A, 107, 709-714.  
20033061 J.B.Munro, R.B.Altman, C.S.Tung, K.Y.Sanbonmatsu, and S.C.Blanchard (2010).
A fast dynamic mode of the EF-G-bound ribosome.
  EMBO J, 29, 770-781.  
19897649 J.Crandall, M.Rodriguez-Lopez, M.Pfeiffer, B.Mortensen, and A.Buskirk (2010).
rRNA mutations that inhibit transfer-messenger RNA activity on stalled ribosomes.
  J Bacteriol, 192, 553-559.  
20235828 J.Frank, and R.L.Gonzalez (2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
  Annu Rev Biochem, 79, 381-412.  
  21072331 J.Frank (2010).
The Ribosome Comes Alive.
  Isr J Chem, 50, 95-98.  
20584915 J.Sengupta, C.Bussiere, J.Pallesen, M.West, A.W.Johnson, and J.Frank (2010).
Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit.
  J Cell Biol, 189, 1079-1086.  
19952067 K.Réblová, F.Rázga, W.Li, H.Gao, J.Frank, and J.Sponer (2010).
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
  Nucleic Acids Res, 38, 1325-1340.  
20400952 L.B.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
  Nat Struct Mol Biol, 17, 555-560.
PDB codes: 3i8f 3i8g 3i8h 3i8i 3i9b 3i9c 3i9d 3i9e
20215430 L.García-Ortega, E.Alvarez-García, J.G.Gavilanes, A.Martínez-del-Pozo, and S.Joseph (2010).
Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding.
  Nucleic Acids Res, 38, 4108-4119.  
19946275 M.B.Feldman, D.S.Terry, R.B.Altman, and S.C.Blanchard (2010).
Aminoglycoside activity observed on single pre-translocation ribosome complexes.
  Nat Chem Biol, 6, 54-62.  
20631789 M.Ehrenberg (2010).
Protein synthesis: Translocation in slow motion.
  Nature, 466, 325-326.  
20705654 M.H.Rhodin, and J.D.Dinman (2010).
A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding.
  Nucleic Acids Res, 38, 8377-8389.  
20529921 M.Saha, M.Levitt, and W.Chiu (2010).
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures.
  Bioinformatics, 26, i301-i309.  
20631791 N.Fischer, A.L.Konevega, W.Wintermeyer, M.V.Rodnina, and H.Stark (2010).
Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.
  Nature, 466, 329-333.  
20022945 T.Yamamoto, Y.Shimizu, T.Ueda, and Y.Shiro (2010).
Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry.
  J Biol Chem, 285, 5646-5652.  
20511136 X.Agirrezabala, and J.Frank (2010).
From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery.
  Hum Genomics, 4, 226-237.  
19095617 A.Devaraj, S.Shoji, E.D.Holbrook, and K.Fredrick (2009).
A role for the 30S subunit E site in maintenance of the translational reading frame.
  RNA, 15, 255-265.  
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.  
19416977 A.S.Spirin (2009).
The ribosome as a conveying thermal ratchet machine.
  J Biol Chem, 284, 21103-21119.  
19536129 C.Ticu, R.Nechifor, B.Nguyen, M.Desrosiers, and K.S.Wilson (2009).
Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome.
  EMBO J, 28, 2053-2065.  
20004163 D.J.Taylor, B.Devkota, A.D.Huang, M.Topf, E.Narayanan, A.Sali, S.C.Harvey, and J.Frank (2009).
Comprehensive molecular structure of the eukaryotic ribosome.
  Structure, 17, 1591-1604.
PDB codes: 3jyv 3jyw 3jyx
19213046 D.M.Hamburg, M.J.Suh, and P.A.Limbach (2009).
Limited proteolysis analysis of the ribosome is affected by subunit association.
  Biopolymers, 91, 410-422.  
18621088 D.P.Giedroc, and P.V.Cornish (2009).
Frameshifting RNA pseudoknots: structure and mechanism.
  Virus Res, 139, 193-208.
PDB codes: 2rp0 2rp1
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.  
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.
  Cell, 136, 261-271.  
19696344 G.Blaha, R.E.Stanley, and T.A.Steitz (2009).
Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
  Science, 325, 966-970.
PDB codes: 3huw 3hux 3huy 3huz
19469554 G.Y.Soung, J.L.Miller, H.Koc, and E.C.Koc (2009).
Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes.
  J Proteome Res, 8, 3390-3402.  
19647434 J.B.Munro, K.Y.Sanbonmatsu, C.M.Spahn, and S.C.Blanchard (2009).
Navigating the ribosome's metastable energy landscape.
  Trends Biochem Sci, 34, 390-400.  
19717422 J.Fei, J.E.Bronson, J.M.Hofman, R.L.Srinivas, C.H.Wiggins, and R.L.Gonzalez (2009).
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation.
  Proc Natl Acad Sci U S A, 106, 15702-15707.  
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.  
19625386 M.H.Mazauric, J.L.Leroy, K.Visscher, S.Yoshizawa, and D.Fourmy (2009).
Footprinting analysis of BWYV pseudoknot-ribosome complexes.
  RNA, 15, 1775-1786.  
19812214 M.H.Mazauric, Y.Seol, S.Yoshizawa, K.Visscher, and D.Fourmy (2009).
Interaction of the HIV-1 frameshift signal with the ribosome.
  Nucleic Acids Res, 37, 7654-7664.  
19339279 M.Prestele, F.Vogel, A.S.Reichert, J.M.Herrmann, and M.Ott (2009).
Mrpl36 Is Important for Generation of Assembly Competent Proteins during Mitochondrial Translation.
  Mol Biol Cell, 20, 2615-2625.  
19595805 M.Simonović, and T.A.Steitz (2009).
A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.
  Biochim Biophys Acta, 1789, 612-623.  
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.  
19190181 P.V.Cornish, D.N.Ermolenko, D.W.Staple, L.Hoang, R.P.Hickerson, H.F.Noller, and T.Ha (2009).
Following movement of the L1 stalk between three functional states in single ribosomes.
  Proc Natl Acad Sci U S A, 106, 2571-2576.  
19595714 R.A.Marshall, C.E.Aitken, and J.D.Puglisi (2009).
GTP hydrolysis by IF2 guides progression of the ribosome into elongation.
  Mol Cell, 35, 37-47.  
19223173 S.C.Blanchard (2009).
Single-molecule observations of ribosome function.
  Curr Opin Struct Biol, 19, 103-109.  
19597483 S.H.Sternberg, J.Fei, N.Prywes, K.A.McGrath, and R.L.Gonzalez (2009).
Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling.
  Nat Struct Mol Biol, 16, 861-868.  
19417061 S.Shoji, N.M.Abdi, R.Bundschuh, and K.Fredrick (2009).
Contribution of ribosomal residues to P-site tRNA binding.
  Nucleic Acids Res, 37, 4033-4042.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
19269332 W.T.Baxter, R.A.Grassucci, H.Gao, and J.Frank (2009).
Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules.
  J Struct Biol, 166, 126-132.  
19696352 W.Zhang, J.A.Dunkle, and J.H.Cate (2009).
Structures of the ribosome in intermediate states of ratcheting.
  Science, 325, 1014-1017.
PDB codes: 3i1m 3i1n 3i1o 3i1p 3i1q 3i1r 3i1s 3i1t 3i1z 3i20 3i21 3i22
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
19545171 X.Shi, K.Chiu, S.Ghosh, and S.Joseph (2009).
Bases in 16S rRNA important for subunit association, tRNA binding, and translocation.
  Biochemistry, 48, 6772-6782.  
19833919 Y.G.Gao, M.Selmer, C.M.Dunham, A.Weixlbaumer, A.C.Kelley, and V.Ramakrishnan (2009).
The structure of the ribosome with elongation factor G trapped in the posttranslocational state.
  Science, 326, 694-699.
PDB codes: 2wri 2wrj 2wrk 2wrl
18177894 A.A.Saraiya, T.N.Lamichhane, C.S.Chow, J.SantaLucia, and P.R.Cunningham (2008).
Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA.
  J Mol Biol, 376, 645-657.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
18824477 A.N.Petrov, A.Meskauskas, S.C.Roshwalb, and J.D.Dinman (2008).
Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit.
  Nucleic Acids Res, 36, 6187-6198.  
18157151 D.A.Costantino, J.S.Pfingsten, R.P.Rambo, and J.S.Kieft (2008).
tRNA-mRNA mimicry drives translation initiation from a viral IRES.
  Nat Struct Mol Biol, 15, 57-64.
PDB code: 3b31
18544041 E.M.Youngman, M.E.McDonald, and R.Green (2008).
Peptide release on the ribosome: mechanism and implications for translational control.
  Annu Rev Microbiol, 62, 353-373.  
18201202 H.Aoki, J.Xu, A.Emili, J.G.Chosay, A.Golshani, and M.C.Ganoza (2008).
Interactions of elongation factor EF-P with the Escherichia coli ribosome.
  FEBS J, 275, 671-681.  
18936244 H.Ishida, and S.Hayward (2008).
Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome.
  Biophys J, 95, 5962-5973.  
18586844 J.A.Kovacs, M.Yeager, and R.Abagyan (2008).
Damped-dynamics flexible fitting.
  Biophys J, 95, 3192-3207.  
18286627 J.B.Munro, A.Vaiana, K.Y.Sanbonmatsu, and S.C.Blanchard (2008).
A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET.
  Biopolymers, 89, 565-577.  
18285480 J.Botet, M.Rodríguez-Mateos, J.P.Ballesta, J.L.Revuelta, and M.Remacha (2008).
A chemical genomic screen in Saccharomyces cerevisiae reveals a role for diphthamidation of translation elongation factor 2 in inhibition of protein synthesis by sordarin.
  Antimicrob Agents Chemother, 52, 1623-1629.  
18471980 J.Fei, P.Kosuri, D.D.MacDougall, and R.L.Gonzalez (2008).
Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation.
  Mol Cell, 30, 348-359.  
18468443 J.S.Kieft (2008).
Viral IRES RNA structures and ribosome interactions.
  Trends Biochem Sci, 33, 274-283.  
18515544 J.S.Pfingsten, and J.S.Kieft (2008).
RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes.
  RNA, 14, 1255-1263.  
18644383 J.Sengupta, J.Nilsson, R.Gursky, M.Kjeldgaard, P.Nissen, and J.Frank (2008).
Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy.
  J Mol Biol, 382, 179-187.
PDB codes: 3dny 3dwu
18270964 K.Voltz, J.Trylska, V.Tozzini, V.Kurkal-Siebert, J.Langowski, and J.Smith (2008).
Coarse-grained force field for the nucleosome from self-consistent multiscaling.
  J Comput Chem, 29, 1429-1439.  
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.  
18567815 M.A.Borovinskaya, S.Shoji, K.Fredrick, and J.H.Cate (2008).
Structural basis for hygromycin B inhibition of protein biosynthesis.
  RNA, 14, 1590-1599.
PDB codes: 3df1 3df2 3df3 3df4
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.  
18084270 M.S.Jurica (2008).
Searching for a wrench to throw into the splicing machine.
  Nat Chem Biol, 4, 3-6.  
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.  
18400176 P.Chandramouli, M.Topf, J.F.Ménétret, N.Eswar, J.J.Cannone, R.R.Gutell, A.Sali, and C.W.Akey (2008).
Structure of the mammalian 80S ribosome at 8.7 A resolution.
  Structure, 16, 535-548.
PDB codes: 2zkq 2zkr
18971332 P.Julián, A.L.Konevega, S.H.Scheres, M.Lázaro, D.Gil, W.Wintermeyer, M.V.Rodnina, and M.Valle (2008).
Structure of ratcheted ribosomes with tRNAs in hybrid states.
  Proc Natl Acad Sci U S A, 105, 16924-16927.  
18538656 P.V.Cornish, D.N.Ermolenko, H.F.Noller, and T.Ha (2008).
Spontaneous intersubunit rotation in single ribosomes.
  Mol Cell, 30, 578-588.  
18518820 R.A.Marshall, C.E.Aitken, M.Dorywalska, and J.D.Puglisi (2008).
Translation at the single-molecule level.
  Annu Rev Biochem, 77, 177-203.  
18824686 R.A.Marshall, M.Dorywalska, and J.D.Puglisi (2008).
Irreversible chemical steps control intersubunit dynamics during translation.
  Proc Natl Acad Sci U S A, 105, 15364-15369.  
18362332 R.N.Evans, G.Blaha, S.Bailey, and T.A.Steitz (2008).
The structure of LepA, the ribosomal back translocase.
  Proc Natl Acad Sci U S A, 105, 4673-4678.
PDB code: 3cb4
18591673 S.E.Walker, S.Shoji, D.Pan, B.S.Cooperman, and K.Fredrick (2008).
Role of hybrid tRNA-binding states in ribosomal translocation.
  Proc Natl Acad Sci U S A, 105, 9192-9197.  
18462671 S.J.Moran, J.F.Flanagan, O.Namy, D.I.Stuart, I.Brierley, and R.J.Gilbert (2008).
The mechanics of translocation: a molecular "spring-and-ratchet" system.
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18391406 S.Kishishita, K.Shimizu, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama, and N.Kunishima (2008).
Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2.
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PDB codes: 1wde 1wng
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.
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PDB codes: 3deg 3qkf 3r4e
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
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18805973 T.Monshupanee, S.T.Gregory, S.Douthwaite, W.Chungjatupornchai, and A.E.Dahlberg (2008).
Mutations in conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications.
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18667704 V.Di Giacco, V.Márquez, Y.Qin, M.Pech, F.J.Triana-Alonso, D.N.Wilson, and K.H.Nierhaus (2008).
Shine-Dalgarno interaction prevents incorporation of noncognate amino acids at the codon following the AUG.
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18502805 V.Hauryliuk, S.Hansson, and M.Ehrenberg (2008).
Cofactor dependent conformational switching of GTPases.
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18836081 V.Hauryliuk, V.A.Mitkevich, N.A.Eliseeva, I.Y.Petrushanko, M.Ehrenberg, and A.A.Makarov (2008).
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18056080 V.Venditti, N.Niccolai, and S.E.Butcher (2008).
Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL.
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19081053 W.Zhang, M.Kimmel, C.M.Spahn, and P.A.Penczek (2008).
Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis.
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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.
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17897673 A.Korostelev, and H.F.Noller (2007).
Analysis of structural dynamics in the ribosome by TLS crystallographic refinement.
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17764954 A.Korostelev, and H.F.Noller (2007).
The ribosome in focus: new structures bring new insights.
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17568775 A.Unbehaun, A.Marintchev, I.B.Lomakin, T.Didenko, G.Wagner, C.U.Hellen, and T.V.Pestova (2007).
Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing.
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17643374 C.Barat, P.P.Datta, V.S.Raj, M.R.Sharma, H.Kaji, A.Kaji, and R.K.Agrawal (2007).
Progression of the ribosome recycling factor through the ribosome dissociates the two ribosomal subunits.
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17128284 C.S.Fraser, and J.A.Doudna (2007).
Structural and mechanistic insights into hepatitis C viral translation initiation.
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18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
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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.
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PDB codes: 2p8w 2p8x 2p8y 2p8z
17442720 D.Luque, I.Saugar, J.F.Rodríguez, N.Verdaguer, D.Garriga, C.S.Martín, J.A.Velázquez-Muriel, B.L.Trus, J.L.Carrascosa, and J.R.Castón (2007).
Infectious bursal disease virus capsid assembly and maturation by structural rearrangements of a transient molecular switch.
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17515906 D.N.Ermolenko, P.C.Spiegel, Z.K.Majumdar, R.P.Hickerson, R.M.Clegg, and H.F.Noller (2007).
The antibiotic viomycin traps the ribosome in an intermediate state of translocation.
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17317625 D.Pan, S.V.Kirillov, and B.S.Cooperman (2007).
Kinetically competent intermediates in the translocation step of protein synthesis.
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17553840 F.Rázga, J.Koca, A.Mokdad, and J.Sponer (2007).
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17088492 G.Hirokawa, H.Kaji, and A.Kaji (2007).
Inhibition of antiassociation activity of translation initiation factor 3 by paromomycin.
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17693476 H.D.Kim, J.D.Puglisi, and S.Chu (2007).
Fluctuations of transfer RNAs between classical and hybrid states.
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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
17209036 H.Yamamoto, N.Nakashima, Y.Ikeda, and T.Uchiumi (2007).
Binding mode of the first aminoacyl-tRNA in translation initiation mediated by Plautia stali intestine virus internal ribosome entry site.
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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.
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18003906 J.Frank, H.Gao, J.Sengupta, N.Gao, and D.J.Taylor (2007).
The process of mRNA-tRNA translocation.
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17434183 J.Nilsson, J.Sengupta, R.Gursky, P.Nissen, and J.Frank (2007).
Comparison of fungal 80 S ribosomes by cryo-EM reveals diversity in structure and conformation of rRNA expansion segments.
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17360328 L.H.Horan, and H.F.Noller (2007).
Intersubunit movement is required for ribosomal translocation.
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17660832 M.A.Borovinskaya, R.D.Pai, W.Zhang, B.S.Schuwirth, J.M.Holton, G.Hirokawa, H.Kaji, A.Kaji, and J.H.Cate (2007).
Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.
  Nat Struct Mol Biol, 14, 727-732.
PDB codes: 2qal 2qam 2qan 2qao 2qb9 2qba 2qbb 2qbc 2qbd 2qbe 2qbf 2qbg 2qbh 2qbi 2qbj 2qbk 2z4k 2z4l 2z4m 2z4n
17704133 M.Léger, D.Dulude, S.V.Steinberg, and L.Brakier-Gingras (2007).
The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift.
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17996252 N.Gao, A.V.Zavialov, M.Ehrenberg, and J.Frank (2007).
Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
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PDB code: 2rdo
17630323 P.C.Spiegel, D.N.Ermolenko, and H.F.Noller (2007).
Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome.
  RNA, 13, 1473-1482.  
17932030 R.Nechifor, M.Murataliev, and K.S.Wilson (2007).
Functional Interactions between the G' Subdomain of Bacterial Translation Factor EF-G and Ribosomal Protein L7/L12.
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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.
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PDB codes: 2e1r 2npf
17179934 S.H.Scheres, H.Gao, M.Valle, G.T.Herman, P.P.Eggermont, J.Frank, and J.M.Carazo (2007).
Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.
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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.
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PDB code: 2om7
17283211 S.V.Steinberg, and Y.I.Boutorine (2007).
G-ribo: a new structural motif in ribosomal RNA.
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17574829 V.Berk, and J.H.Cate (2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
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16855312 A.Liljas (2006).
On the complementarity of methods in structural biology.
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16556933 A.Pulk, U.Maiväli, and J.Remme (2006).
Identification of nucleotides in E. coli 16S rRNA essential for ribosome subunit association.
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16940356 B.Wilden, A.Savelsbergh, M.V.Rodnina, and W.Wintermeyer (2006).
Role and timing of GTP binding and hydrolysis during EF-G-dependent tRNA translocation on the ribosome.
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16929303 C.B.Andersen, T.Becker, M.Blau, M.Anand, M.Halic, B.Balar, T.Mielke, T.Boesen, J.S.Pedersen, C.M.Spahn, T.G.Kinzy, G.R.Andersen, and R.Beckmann (2006).
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
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PDB codes: 2iw3 2iwh 2ix3 2ix8
16711863 C.Y.Lee (2006).
Mass fractal dimension of the ribosome and implication of its dynamic characteristics.
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16532005 D.Pan, S.Kirillov, C.M.Zhang, Y.M.Hou, and B.S.Cooperman (2006).
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16689630 F.Tama, and C.L.Brooks (2006).
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.
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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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16843893 J.A.Velazquez-Muriel, M.Valle, A.Santamaría-Pang, I.A.Kakadiaris, and J.M.Carazo (2006).
Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies.
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16489185 J.S.Feinberg, and S.Joseph (2006).
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  RNA, 12, 580-588.  
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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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16538608 K.Réblová, F.Lankas, F.Rázga, M.V.Krasovska, J.Koca, and J.Sponer (2006).
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations.
  Biopolymers, 82, 504-520.  
16565414 L.D.Kapp, S.E.Kolitz, and J.R.Lorsch (2006).
Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation.
  RNA, 12, 751-764.  
17115051 M.Schüler, S.R.Connell, A.Lescoute, J.Giesebrecht, M.Dabrowski, B.Schroeer, T.Mielke, P.A.Penczek, E.Westhof, and C.M.Spahn (2006).
Structure of the ribosome-bound cricket paralysis virus IRES RNA.
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PDB code: 2noq
16619019 N.Gao, and J.Frank (2006).
A library of RNA bridges.
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16582919 O.Rackham, K.Wang, and J.W.Chin (2006).
Functional epitopes at the ribosome subunit interface.
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17000775 R.Rakauskaite, and J.D.Dinman (2006).
An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome.
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16501572 S.Dorner, J.L.Brunelle, D.Sharma, and R.Green (2006).
The hybrid state of tRNA binding is an authentic translation elongation intermediate.
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16950778 T.Komoda, N.S.Sato, S.S.Phelps, N.Namba, S.Joseph, and T.Suzuki (2006).
The A-site finger in 23 S rRNA acts as a functional attenuator for translocation.
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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
16292341 A.Savelsbergh, D.Mohr, U.Kothe, W.Wintermeyer, and M.V.Rodnina (2005).
Control of phosphate release from elongation factor G by ribosomal protein L7/12.
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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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15949442 A.V.Zavialov, V.V.Hauryliuk, and M.Ehrenberg (2005).
Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G.
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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.
  Science, 310, 827-834.
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.
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15985151 C.S.Fraser, and J.W.Hershey (2005).
Movement in ribosome translocation.
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16271893 D.Boehringer, R.Thermann, A.Ostareck-Lederer, J.D.Lewis, and H.Stark (2005).
Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES.
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PDB code: 2agn
15616575 D.N.Wilson, F.Schluenzen, J.M.Harms, T.Yoshida, T.Ohkubo, R.Albrecht, J.Buerger, Y.Kobayashi, and P.Fucini (2005).
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
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PDB code: 1y69
15872184 F.Bélanger, G.Théberge-Julien, P.R.Cunningham, and L.Brakier-Gingras (2005).
A functional relationship between helix 1 and the 900 tetraloop of 16S ribosomal RNA within the bacterial ribosome.
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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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16141058 H.F.Noller (2005).
RNA structure: reading the ribosome.
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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.
  Structure, 13, 401-406.  
  18074004 J.D.Dinman (2005).
5S rRNA: Structure and Function from Head to Toe.
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15501947 J.Elf, and M.Ehrenberg (2005).
Near-critical behavior of aminoacyl-tRNA pools in E. coli at rate-limiting supply of amino acids.
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16271881 J.H.Cate (2005).
The ins and outs of protein synthesis.
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Elongation factors on the ribosome.
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15951386 J.Trylska, V.Tozzini, and J.A.McCammon (2005).
Exploring global motions and correlations in the ribosome.
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16307924 K.G.McGarry, S.E.Walker, H.Wang, and K.Fredrick (2005).
Destabilization of the P site codon-anticodon helix results from movement of tRNA into the P/E hybrid state within the ribosome.
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Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
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PDB codes: 1zn0 1zn1
16177132 N.M.Abdi, and K.Fredrick (2005).
Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli.
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16174429 O.Llorca (2005).
Introduction to 3D reconstruction of macromolecules using single particle electron microscopy.
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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.
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PDB code: 2bcw
16243787 P.V.Sergiev, D.V.Lesnyak, S.V.Kiparisov, D.E.Burakovsky, A.A.Leonov, A.A.Bogdanov, R.Brimacombe, and O.A.Dontsova (2005).
Function of the ribosomal E-site: a mutagenesis study.
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14707145 A.J.Herr, N.M.Wills, C.C.Nelson, R.F.Gesteland, and J.F.Atkins (2004).
Factors that influence selection of coding resumption sites in translational bypassing: minimal conventional peptidyl-tRNA:mRNA pairing can suffice.
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15315759 C.M.Spahn, E.Jan, A.Mulder, R.A.Grassucci, P.Sarnow, and J.Frank (2004).
Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
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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.
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PDB codes: 1s1h 1s1i
14681582 D.Rodriguez-Correa, and A.E.Dahlberg (2004).
Genetic evidence against the 16S ribosomal RNA helix 27 conformational switch model.
  RNA, 10, 28-33.  
14681589 D.Sharma, D.R.Southworth, and R.Green (2004).
EF-G-independent reactivity of a pre-translocation-state ribosome complex with the aminoacyl tRNA substrate puromycin supports an intermediate (hybrid) state of tRNA binding.
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14960595 E.V.Bocharov, A.G.Sobol, K.V.Pavlov, D.M.Korzhnev, V.A.Jaravine, A.T.Gudkov, and A.S.Arseniev (2004).
From structure and dynamics of protein L7/L12 to molecular switching in ribosome.
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PDB codes: 1rqs 1rqt 1rqu 1rqv
15465319 E.V.Orlova, and H.R.Saibil (2004).
Structure determination of macromolecular assemblies by single-particle analysis of cryo-electron micrographs.
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15274086 J.Trylska, R.Konecny, F.Tama, C.L.Brooks, and J.A.McCammon (2004).
Ribosome motions modulate electrostatic properties.
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15525706 K.Semrad, R.Green, and R.Schroeder (2004).
RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli.
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15100432 M.B.Sagar, L.Lucast, and J.A.Doudna (2004).
Conserved but nonessential interaction of SRP RNA with translation factor EF-G.
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15102450 P.W.Haebel, S.Gutmann, and N.Ban (2004).
Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs.
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15068803 R.J.Gilbert, P.Fucini, S.Connell, S.D.Fuller, K.H.Nierhaus, C.V.Robinson, C.M.Dobson, and D.I.Stuart (2004).
Three-dimensional structures of translating ribosomes by Cryo-EM.
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15520810 R.Schroeder, A.Barta, and K.Semrad (2004).
Strategies for RNA folding and assembly.
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15317937 S.C.Blanchard, H.D.Kim, R.L.Gonzalez, J.D.Puglisi, and S.Chu (2004).
tRNA dynamics on the ribosome during translation.
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15139808 S.Subramaniam, and J.L.Milne (2004).
Three-dimensional electron microscopy at molecular resolution.
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15228531 T.Fujiwara, K.Ito, T.Yamami, and Y.Nakamura (2004).
Ribosome recycling factor disassembles the post-termination ribosomal complex independent of the ribosomal translocase activity of elongation factor G.
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15037769 U.Maiväli, and J.Remme (2004).
Definition of bases in 23S rRNA essential for ribosomal subunit association.
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15598826 W.Huggins, and P.Wollenzien (2004).
A 16S rRNA-tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome.
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Peptidyl-tRNA regulates the GTPase activity of translation factors.
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Divergent tRNA-like element supports initiation, elongation, and termination of protein biosynthesis.
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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.