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PDBsum entry 1ffk

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protein dna_rna metals links
Ribosome PDB id
1ffk
Jmol
Contents
Protein chains
237 a.a.* *
337 a.a.* *
246 a.a.* *
140 a.a.* *
118 a.a.* *
157 a.a.* *
142 a.a.* *
132 a.a.* *
194 a.a.* *
143 a.a.* *
186 a.a.* *
115 a.a.* *
143 a.a.* *
95 a.a.* *
150 a.a.* *
78 a.a.* *
119 a.a.* *
53 a.a.* *
65 a.a.* *
154 a.a.* *
85 a.a.* *
143 a.a.* *
73 a.a.* *
56 a.a.* *
31 a.a.* *
92 a.a.* *
172 a.a.* *
DNA/RNA
Metals
_CD ×4
_MG ×2
__K
Waters ×6
* Residue conservation analysis
* C-alpha coords only
PDB id:
1ffk
Name: Ribosome
Title: Crystal structure of the large ribosomal subunit from haloarcula marismortui at 2.4 angstrom resolution
Structure: 23s rrna. Chain: 0. 5s rrna. Chain: 9. Ribosomal protein l2. Chain: a. Synonym: 50s ribosomal protein l2p, hmal2, hl4. Ribosomal protein l3. Chain: b.
Source: Haloarcula marismortui. Organism_taxid: 2238. Other_details: cultured cells. Other_details: cultured cells
Resolution:
2.40Å     R-factor:   0.252     R-free:   0.261
Authors: N.Ban,P.Nissen,J.Hansen,P.B.Moore,T.A.Steitz
Key ref:
N.Ban et al. (2000). The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 289, 905-920. PubMed id: 10937989 DOI: 10.1126/science.289.5481.905
Date:
25-Jul-00     Release date:   14-Aug-00    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20276  (RL2_HALMA) -  50S ribosomal protein L2
Seq:
Struc:
240 a.a.
237 a.a.*
Protein chain
Pfam   ArchSchema ?
P20279  (RL3_HALMA) -  50S ribosomal protein L3
Seq:
Struc:
338 a.a.
337 a.a.*
Protein chain
Pfam   ArchSchema ?
P12735  (RL4_HALMA) -  50S ribosomal protein L4
Seq:
Struc:
246 a.a.
246 a.a.*
Protein chain
Pfam   ArchSchema ?
P14124  (RL5_HALMA) -  50S ribosomal protein L5
Seq:
Struc:
177 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P12743  (RL7A_HALMA) -  50S ribosomal protein L7Ae
Seq:
Struc:
120 a.a.
118 a.a.*
Protein chain
Pfam   ArchSchema ?
P60617  (RL10_HALMA) -  50S ribosomal protein L10e
Seq:
Struc:
177 a.a.
157 a.a.*
Protein chain
Pfam   ArchSchema ?
P29198  (RL13_HALMA) -  50S ribosomal protein L13
Seq:
Struc:
145 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P22450  (RL14_HALMA) -  50S ribosomal protein L14
Seq:
Struc:
132 a.a.
132 a.a.
Protein chain
Pfam   ArchSchema ?
P60618  (RL15E_HALMA) -  50S ribosomal protein L15e
Seq:
Struc:
196 a.a.
194 a.a.*
Protein chain
Pfam   ArchSchema ?
P12737  (RL15_HALMA) -  50S ribosomal protein L15P
Seq:
Struc:
165 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P14123  (RL18_HALMA) -  50S ribosomal protein L18P
Seq:
Struc:
187 a.a.
186 a.a.
Protein chain
Pfam   ArchSchema ?
P12733  (RL18E_HALMA) -  50S ribosomal protein L18e
Seq:
Struc:
116 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P14119  (RL19_HALMA) -  50S ribosomal protein L19e
Seq:
Struc:
149 a.a.
143 a.a.*
Protein chain
Pfam   ArchSchema ?
P12734  (RL21_HALMA) -  50S ribosomal protein L21e
Seq:
Struc:
96 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P10970  (RL22_HALMA) -  50S ribosomal protein L22P
Seq:
Struc:
155 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P12732  (RL23_HALMA) -  50S ribosomal protein L23P
Seq:
Struc:
85 a.a.
78 a.a.
Protein chain
Pfam   ArchSchema ?
P10972  (RL24_HALMA) -  50S ribosomal protein L24P
Seq:
Struc:
120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P14116  (RL24E_HALMA) -  50S ribosomal protein L24e
Seq:
Struc:
67 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
P10971  (RL29_HALMA) -  50S ribosomal protein L29P
Seq:
Struc:
71 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P14121  (RL30_HALMA) -  50S ribosomal protein L30P
Seq:
Struc:
154 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P18138  (RL31_HALMA) -  50S ribosomal protein L31e
Seq:
Struc:
92 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
P12736  (RL32_HALMA) -  50S ribosomal protein L32e
Seq:
Struc:
241 a.a.
143 a.a.*
Protein chain
No UniProt id for this chain
Struc: 73 a.a.
Protein chain
Pfam   ArchSchema ?
P32410  (RL37_HALMA) -  50S ribosomal protein L37e
Seq:
Struc:
57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P22452  (RL39_HALMA) -  50S ribosomal protein L39e
Seq:
Struc:
50 a.a.
31 a.a.*
Protein chain
Pfam   ArchSchema ?
P32411  (RL44_HALMA) -  50S ribosomal protein L44e
Seq:
Struc:
92 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
P14135  (RL6_HALMA) -  50S ribosomal protein L6
Seq:
Struc:
178 a.a.
172 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 180 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     ribosome biogenesis   2 terms 
  Biochemical function     structural constituent of ribosome     9 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.289.5481.905 Science 289:905-920 (2000)
PubMed id: 10937989  
 
 
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
N.Ban, P.Nissen, J.Hansen, P.B.Moore, T.A.Steitz.
 
  ABSTRACT  
 
The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotides and 27 of its 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Proteins are abundant everywhere on its surface except in the active site where peptide bond formation occurs and where it contacts the small subunit. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Portions of the experimental 2.4 Å resolution electron density map. (A) A stereo view of a junction between 23S rRNA domains II, III, IV, and V having a complex structure that is clearly interpretable. The electron density is contoured at 2 . The bases are white and the backbones are colored by domain as specified in Fig. 4. (B) The extended region of L3 interacting with its surrounding RNA, where the red RNA density is contoured at 2 and the blue protein density is contoured at 1.5 . (C) Detail in the L2 region showing a bound Mg2+ ion. (D) Detail from L2 showing amino acid side chains. (E) Helices 94 through 97 from domain VI. The red contour level is at 2 , and the yellow contour at 6 shows the positions of the higher electron density phosphate groups.
Figure 2.
Fig. 2. The H. marismortui large ribosomal subunit in the rotated crown view. The L7/L12 stalk is to the right, the L1 stalk is to the left, and the central protuberance (CP) is at the top. In this view, the surface of the subunit that interacts with the small subunit faces the reader. RNA is shown in gray in a pseudo-space-filling rendering. The backbones of the proteins visible are rendered in gold. The Yarus inhibitor bound to the peptidyl transferase site of the subunit is indicated in green (64). The particle is approximately 250 Å across.
 
  The above figures are reprinted by permission from the AAAs: Science (2000, 289, 905-920) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
  Proc Natl Acad Sci U S A, 107, 19748-19753.
PDB codes: 3izb 3izc 3izd 3ize 3izf 3izs
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  Nucleic Acids Res, 38, 3388-3398.
PDB code: 2khy
20211929 J.Y.Dutheil, F.Jossinet, and E.Westhof (2010).
Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
  Mol Biol Evol, 27, 1868-1876.  
20403320 K.Fredrick, and M.Ibba (2010).
How the sequence of a gene can tune its translation.
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20117091 K.Ito, S.Chiba, and K.Pogliano (2010).
Divergent stalling sequences sense and control cellular physiology.
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20404211 K.S.Keating, and A.M.Pyle (2010).
Semiautomated model building for RNA crystallography using a directed rotameric approach.
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Arrangement of 3D structural motifs in ribosomal RNA.
  Nucleic Acids Res, 38, 3512-3522.  
19926724 K.T.Gagnon, X.Zhang, G.Qu, S.Biswas, J.Suryadi, B.A.Brown, and E.S.Maxwell (2010).
Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif.
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20075606 K.Watanabe (2010).
Unique features of animal mitochondrial translation systems. The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases.
  Proc Jpn Acad Ser B Phys Biol Sci, 86, 11-39.  
19754142 M.A.Ditzler, M.Otyepka, J.Sponer, and N.G.Walter (2010).
Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.
  Acc Chem Res, 43, 40-47.  
21079586 M.Bucci, C.Goodman, and T.L.Sheppard (2010).
A decade of chemical biology.
  Nat Chem Biol, 6, 847-854.  
20616058 M.D.Daugherty, D.S.Booth, B.Jayaraman, Y.Cheng, and A.D.Frankel (2010).
HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes.
  Proc Natl Acad Sci U S A, 107, 12481-12486.  
20466811 M.Falb, I.Amata, F.Gabel, B.Simon, and T.Carlomagno (2010).
Structure of the K-turn U4 RNA: a combined NMR and SANS study.
  Nucleic Acids Res, 38, 6274-6285.
PDB code: 2xeb
20038632 M.G.Gagnon, and S.V.Steinberg (2010).
The adenosine wedge: a new structural motif in ribosomal RNA.
  RNA, 16, 375-381.  
20139416 M.G.Gagnon, Y.I.Boutorine, and S.V.Steinberg (2010).
Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome.
  Nucleic Acids Res, 38, 3441-3453.  
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.  
20056148 M.Rusu, and S.Birmanns (2010).
Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.
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Ligand-pKa shifts through metals: potential relevance to ribozyme chemistry.
  Chem Biodivers, 5, 1455-1474.  
18218711 B.Wu, A.Yee, Y.J.Huang, T.A.Ramelot, J.R.Cort, A.Semesi, J.W.Jung, W.Lee, G.T.Montelione, M.A.Kennedy, and C.H.Arrowsmith (2008).
The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain.
  Protein Sci, 17, 583-588.
PDB code: 1rq6
18218710 B.Wu, J.Lukin, A.Yee, A.Lemak, A.Semesi, T.A.Ramelot, M.A.Kennedy, and C.H.Arrowsmith (2008).
Solution structure of ribosomal protein L40E, a unique C4 zinc finger protein encoded by archaeon Sulfolobus solfataricus.
  Protein Sci, 17, 589-596.
PDB code: 2ayj
19098107 C.Davidovich, A.Bashan, and A.Yonath (2008).
Structural basis for cross-resistance to ribosomal PTC antibiotics.
  Proc Natl Acad Sci U S A, 105, 20665-20670.  
18158305 C.Geary, S.Baudrey, and L.Jaeger (2008).
Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors.
  Nucleic Acids Res, 36, 1138-1152.  
18480044 C.J.Daniel, B.Conti, A.E.Johnson, and W.R.Skach (2008).
Control of translocation through the Sec61 translocon by nascent polypeptide structure within the ribosome.
  J Biol Chem, 283, 20864-20873.  
18683165 C.Voisset, J.Y.Thuret, D.Tribouillard-Tanvier, S.J.Saupe, and M.Blondel (2008).
Tools for the study of ribosome-borne protein folding activity.
  Biotechnol J, 3, 1033-1040.  
17981968 C.Wicker-Planquart, A.E.Foucher, M.Louwagie, R.A.Britton, and J.M.Jault (2008).
Interactions of an essential Bacillus subtilis GTPase, YsxC, with ribosomes.
  J Bacteriol, 190, 681-690.  
18482701 D.A.Kingery, E.Pfund, R.M.Voorhees, K.Okuda, I.Wohlgemuth, D.E.Kitchen, M.V.Rodnina, and S.A.Strobel (2008).
An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction.
  Chem Biol, 15, 493-500.  
18282091 D.L.Theobald, and D.S.Wuttke (2008).
Accurate structural correlations from maximum likelihood superpositions.
  PLoS Comput Biol, 4, e43.  
18755052 D.M.Lilley (2008).
Analysis of branched nucleic acid structure using comparative gel electrophoresis.
  Q Rev Biophys, 41, 1.  
17947322 D.Piekna-Przybylska, W.A.Decatur, and M.J.Fournier (2008).
The 3D rRNA modification maps database: with interactive tools for ribosome analysis.
  Nucleic Acids Res, 36, D178-D183.  
18824514 D.Rodriguez-Correa, and A.E.Dahlberg (2008).
Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus.
  RNA, 14, 2314-2318.  
19436497 E.H.Egelman (2008).
Problems in fitting high resolution structures into electron microscopic reconstructions.
  HFSP J, 2, 324-331.  
18755835 E.Purta, K.H.Kaminska, J.M.Kasprzak, J.M.Bujnicki, and S.Douthwaite (2008).
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.
  RNA, 14, 2234-2244.  
18560149 F.Pavelcik, and B.Schneider (2008).
Building of RNA and DNA double helices into electron density.
  Acta Crystallogr D Biol Crystallogr, 64, 620-626.  
18455733 G.Blaha, G.Gürel, S.J.Schroeder, P.B.Moore, and T.A.Steitz (2008).
Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.
  J Mol Biol, 379, 505-519.
PDB codes: 3cc2 3cc4 3cc7 3cce 3ccj 3ccl 3ccm 3ccq 3ccr 3ccs 3ccu 3ccv 3cd6
18786404 G.Shaw, J.Gan, Y.N.Zhou, H.Zhi, P.Subburaman, R.Zhang, A.Joachimiak, D.J.Jin, and X.Ji (2008).
Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription.
  Structure, 16, 1417-1427.
PDB code: 3dmq
18625614 H.David-Eden, and Y.Mandel-Gutfreund (2008).
Revealing unique properties of the ribosome using a network based analysis.
  Nucleic Acids Res, 36, 4641-4652.  
18844986 H.Grosjean, C.Gaspin, C.Marck, W.A.Decatur, and V.de Crécy-Lagard (2008).
RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.
  BMC Genomics, 9, 470.  
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.  
18607001 H.Van Melckebeke, M.Devany, C.Di Primo, F.Beaurain, J.J.Toulmé, D.L.Bryce, and J.Boisbouvier (2008).
Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex.
  Proc Natl Acad Sci U S A, 105, 9210-9215.
PDB code: 2rn1
17255009 I.D.Campbell (2008).
The Croonian lecture 2006. Structure of the living cell.
  Philos Trans R Soc Lond B Biol Sci, 363, 2379-2391.  
18523488 I.J.Chen, I.A.Wang, L.R.Tai, and A.Lin (2008).
The role of expansion segment of human ribosomal protein L35 in nuclear entry, translation activity, and endoplasmic reticulum docking.
  Biochem Cell Biol, 86, 271-277.  
18996893 I.Lebars, P.Legrand, A.Aimé, N.Pinaud, S.Fribourg, and C.Di Primo (2008).
Exploring TAR-RNA aptamer loop-loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance.
  Nucleic Acids Res, 36, 7146-7156.
PDB code: 2jlt
19019145 J.C.Chiou, X.P.Li, M.Remacha, J.P.Ballesta, and N.E.Tumer (2008).
The ribosomal stalk is required for ribosome binding, depurination of the rRNA and cytotoxicity of ricin A chain in Saccharomyces cerevisiae.
  Mol Microbiol, 70, 1441-1452.  
19049467 J.E.Johnson, and C.G.Hoogstraten (2008).
Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.
  J Am Chem Soc, 130, 16757-16769.  
18256246 J.Esguerra, J.Warringer, and A.Blomberg (2008).
Functional importance of individual rRNA 2'-O-ribose methylations revealed by high-resolution phenotyping.
  RNA, 14, 649-656.  
18468905 J.Heredia-Moya, and K.L.Kirk (2008).
Synthesis of beta-(S-methyl)thioaspartic acid and derivatives.
  Bioorg Med Chem, 16, 5908-5913.  
18406324 J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, and P.Fucini (2008).
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
  Mol Cell, 30, 26-38.
PDB codes: 2zjp 2zjq 2zjr 3cf5
20107615 J.P.Schmidt, S.L.Delp, M.A.Sherman, C.A.Taylor, V.S.Pande, and R.B.Altman (2008).
The Simbios National Center: Systems Biology in Motion.
  Proc IEEE Inst Electr Electron Eng, 96, 1266-1280.  
18192612 J.S.Richardson, B.Schneider, L.W.Murray, G.J.Kapral, R.M.Immormino, J.J.Headd, D.C.Richardson, D.Ham, E.Hershkovits, L.D.Williams, K.S.Keating, A.M.Pyle, D.Micallef, J.Westbrook, and H.M.Berman (2008).
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
  RNA, 14, 465-481.  
18761469 J.Shin, W.Lee, and W.Lee (2008).
Structural proteomics by NMR spectroscopy.
  Expert Rev Proteomics, 5, 589-601.  
18464974 J.Sponer, K.E.Riley, and P.Hobza (2008).
Nature and magnitude of aromatic stacking of nucleic acid bases.
  Phys Chem Chem Phys, 10, 2595-2610.  
18376982 J.Zhang, M.Lin, R.Chen, W.Wang, and J.Liang (2008).
Discrete state model and accurate estimation of loop entropy of RNA secondary structures.
  J Chem Phys, 128, 125107.  
18957331 K.B.Hall (2008).
RNA in motion.
  Curr Opin Chem Biol, 12, 612-618.  
18637734 K.Bakowska-Zywicka, A.M.Kietrys, and T.Twardowski (2008).
Antisense oligonucleotides targeting universally conserved 26S rRNA domains of plant ribosomes at different steps of polypeptide elongation.
  Oligonucleotides, 18, 175-186.  
18957409 K.J.Webb, A.Laganowsky, J.P.Whitelegge, and S.G.Clarke (2008).
Identification of two SET domain proteins required for methylation of lysine residues in yeast ribosomal protein Rpl42ab.
  J Biol Chem, 283, 35561-35568.  
19079550 K.N.Rao, S.K.Burley, and S.Swaminathan (2008).
UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function.
  PLoS ONE, 3, e3903.
PDB codes: 2nrq 2nwu 2ogk 2pzz
18829863 K.Peisker, D.Braun, T.Wölfle, J.Hentschel, U.Fünfschilling, G.Fischer, A.Sickmann, and S.Rospert (2008).
Ribosome-associated complex binds to ribosomes in close proximity of Rpl31 at the exit of the polypeptide tunnel in yeast.
  Mol Biol Cell, 19, 5279-5288.  
18779563 K.Yang, L.Zhang, T.Xu, A.Heroux, and R.Zhao (2008).
Crystal structure of the beta-finger domain of Prp8 reveals analogy to ribosomal proteins.
  Proc Natl Acad Sci U S A, 105, 13817-13822.
PDB code: 3e66
18754628 L.C.Palmer, and S.I.Stupp (2008).
Molecular self-assembly into one-dimensional nanostructures.
  Acc Chem Res, 41, 1674-1684.  
18951096 L.Garcia-Ortega, J.Stephen, and S.Joseph (2008).
Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation.
  Mol Cell, 32, 292-299.  
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.  
18369182 M.Beringer (2008).
Modulating the activity of the peptidyl transferase center of the ribosome.
  RNA, 14, 795-801.  
18441029 M.Chruszcz, A.Wlodawer, and W.Minor (2008).
Determination of protein structures--a series of fortunate events.
  Biophys J, 95, 1-9.
PDB code: 3pzw
18922466 M.D.Daugherty, I.D'Orso, and A.D.Frankel (2008).
A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA.
  Mol Cell, 31, 824-834.  
18586934 M.G.Lawrence, L.Lindahl, and J.M.Zengel (2008).
Effects on translation pausing of alterations in protein and RNA components of the ribosome exit tunnel.
  J Bacteriol, 190, 5862-5869.  
18538657 M.Johansson, E.Bouakaz, M.Lovmar, and M.Ehrenberg (2008).
The kinetics of ribosomal peptidyl transfer revisited.
  Mol Cell, 30, 589-598.  
17921499 M.Popenda, M.Blazewicz, M.Szachniuk, and R.W.Adamiak (2008).
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures.
  Nucleic Acids Res, 36, D386-D391.  
18193063 M.Rogalski, D.Karcher, and R.Bock (2008).
Superwobbling facilitates translation with reduced tRNA sets.
  Nat Struct Mol Biol, 15, 192-198.  
17694311 M.Sarver, C.L.Zirbel, J.Stombaugh, A.Mokdad, and N.B.Leontis (2008).
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.
  J Math Biol, 56, 215-252.  
18400172 M.Selmer, and A.Liljas (2008).
Exit biology: battle for the nascent chain.
  Structure, 16, 498-500.  
18818369 M.Simonović, and T.A.Steitz (2008).
Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.
  RNA, 14, 2372-2378.
PDB codes: 3cma 3cme
18441048 O.Fedorova, and A.M.Pyle (2008).
A conserved element that stabilizes the group II intron active site.
  RNA, 14, 1048-1056.  
18453695 O.Pasternak, A.Bujacz, J.Biesiadka, G.Bujacz, M.Sikorski, and M.Jaskolski (2008).
MAD phasing using the (Ta6Br12)2+ cluster: a retrospective study.
  Acta Crystallogr D Biol Crystallogr, 64, 595-606.
PDB code: 3c0v
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
17938928 P.Clote (2008).
Introduction to special issue on RNA.
  J Math Biol, 56, 3.  
18946046 P.M.Petrone, C.D.Snow, D.Lucent, and V.S.Pande (2008).
Side-chain recognition and gating in the ribosome exit tunnel.
  Proc Natl Acad Sci U S A, 105, 16549-16554.  
18566829 R.F.Degenhardt, and P.C.Bonham-Smith (2008).
Transcript profiling demonstrates absence of dosage compensation in Arabidopsis following loss of a single RPL23a paralog.
  Planta, 228, 627-640.  
18203742 R.Rakauskaite, and J.D.Dinman (2008).
rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance.
  Nucleic Acids Res, 36, 1497-1507.  
17981525 R.Russell (2008).
RNA misfolding and the action of chaperones.
  Front Biosci, 13, 1.  
18268024 S.C.Abeysirigunawardena, and C.S.Chow (2008).
pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA.
  RNA, 14, 782-792.  
18401893 S.Chakraborty, S.Modi, and Y.Krishnan (2008).
The RNA2-PNA2 hybrid i-motif-a novel RNA-based building block.
  Chem Commun (Camb), (), 70-72.  
18025251 S.M.Toh, L.Xiong, T.Bae, and A.S.Mankin (2008).
The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA.
  RNA, 14, 98.  
18573090 S.R.Holbrook (2008).
Structural principles from large RNAs.
  Annu Rev Biophys, 37, 445-464.  
  18259060 S.Rangarajan, J.Jeyakanthan, P.Mridula, K.Sakamoto, Y.Kitamura, Y.Agari, A.Shinkai, A.Ebihara, S.Kuramitsu, S.Yokoyama, and K.Sekar (2008).
Crystallization and preliminary crystallographic studies of L30e, a ribosomal protein from Methanocaldococcus jannaschii (MJ1044).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 102-104.  
17657587 S.Shakil, R.Khan, R.Zarrilli, and A.U.Khan (2008).
Aminoglycosides versus bacteria--a description of the action, resistance mechanism, and nosocomial battleground.
  J Biomed Sci, 15, 5.  
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
  Nat Rev Mol Cell Biol, 9, 242-253.  
18391966 T.Bornemann, J.Jöckel, M.V.Rodnina, and W.Wintermeyer (2008).
Signal sequence-independent membrane targeting of ribosomes containing short nascent peptides within the exit tunnel.
  Nat Struct Mol Biol, 15, 494-499.  
18430223 T.F.Smith, J.C.Lee, R.R.Gutell, and H.Hartman (2008).
The origin and evolution of the ribosome.
  Biol Direct, 3, 16.  
18399722 T.Herman, S.Colton, and M.Franzen (2008).
Rethinking outreach: teaching the process of science through modeling.
  PLoS Biol, 6, e86.  
18456707 T.Yokoyama, and T.Suzuki (2008).
Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments.
  Nucleic Acids Res, 36, 3539-3551.  
18843295 V.Pena, A.Rozov, P.Fabrizio, R.Lührmann, and M.C.Wahl (2008).
Structure and function of an RNase H domain at the heart of the spliceosome.
  EMBO J, 27, 2929-2940.
PDB codes: 3e9l 3e9o 3e9p
18937251 W.C.Horng, Y.H.Yen, and Y.C.Chang (2008).
A novel solid phase- and chemical crosslinking-based technology for determining protein localization in biological supramolecules.
  Proteomics, 8, 4642-4646.  
18600227 X.J.Lu, and W.K.Olson (2008).
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.
  Nat Protoc, 3, 1213-1227.  
17401565 X.Wang, G.Kapral, L.Murray, D.Richardson, J.Richardson, and J.Snoeyink (2008).
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
  J Math Biol, 56, 253-278.  
18435545 Y.Lin, and C.L.Kielkopf (2008).
X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines.
  Biochemistry, 47, 5503-5514.
PDB codes: 3cgp 3cgq 3cgr 3cgs
18957492 Y.Xin, C.Laing, N.B.Leontis, and T.Schlick (2008).
Annotation of tertiary interactions in RNA structures reveals variations and correlations.
  RNA, 14, 2465-2477.  
17105995 A.Barkan, L.Klipcan, O.Ostersetzer, T.Kawamura, Y.Asakura, and K.P.Watkins (2007).
The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein.
  RNA, 13, 55-64.  
17332014 A.Cléry, V.Bourguignon-Igel, C.Allmang, A.Krol, and C.Branlant (2007).
An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the selenocysteine incorporation machinery.
  Nucleic Acids Res, 35, 1868-1884.  
17145781 A.Cléry, V.Senty-Ségault, F.Leclerc, H.A.Raué, and C.Branlant (2007).
Analysis of sequence and structural features that identify the B/C motif of U3 small nucleolar RNA as the recognition site for the Snu13p-Rrp9p protein pair.
  Mol Cell Biol, 27, 1191-1206.  
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.  
17764954 A.Korostelev, and H.F.Noller (2007).
The ribosome in focus: new structures bring new insights.
  Trends Biochem Sci, 32, 434-441.  
17386264 A.Meskauskas, and J.D.Dinman (2007).
Ribosomal protein L3: gatekeeper to the A site.
  Mol Cell, 25, 877-888.  
17379815 A.V.Manuilov, S.S.Hixson, and R.A.Zimmermann (2007).
New photoreactive tRNA derivatives for probing the peptidyl transferase center of the ribosome.
  RNA, 13, 793-800.  
17360517 C.Davidovich, A.Bashan, T.Auerbach-Nevo, R.D.Yaggie, R.R.Gontarek, and A.Yonath (2007).
Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.
  Proc Natl Acad Sci U S A, 104, 4291-4296.
PDB codes: 2ogm 2ogn 2ogo
17806104 C.G.Hoogstraten, and M.Sumita (2007).
Structure-function relationships in RNA and RNP enzymes: recent advances.
  Biopolymers, 87, 317-328.  
17584789 C.L.Ross, R.R.Patel, T.C.Mendelson, and V.C.Ware (2007).
Functional conservation between structurally diverse ribosomal proteins from Drosophila melanogaster and Saccharomyces cerevisiae: fly L23a can substitute for yeast L25 in ribosome assembly and function.
  Nucleic Acids Res, 35, 4503-4514.  
17146803 C.Shammas, J.A.Donarski, and V.Ramesh (2007).
NMR structure of the peptidyl transferase RNA inhibitor antibiotic amicetin.
  Magn Reson Chem, 45, 133-141.  
18075576 C.V.Robinson, A.Sali, and W.Baumeister (2007).
The molecular sociology of the cell.
  Nature, 450, 973-982.  
17914224 D.Bhattacharyya, S.C.Koripella, A.Mitra, V.B.Rajendran, and B.Sinha (2007).
Theoretical analysis of noncanonical base pairing interactions in RNA molecules.
  J Biosci, 32, 809-825.  
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
17283215 D.Piekna-Przybylska, W.A.Decatur, and M.J.Fournier (2007).
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA.
  RNA, 13, 305-312.  
17308345 D.S.Chan, L.O.Chu, K.M.Lee, P.H.Too, K.W.Ma, K.H.Sze, G.Zhu, P.C.Shaw, and K.B.Wong (2007).
Interaction between trichosanthin, a ribosome-inactivating protein, and the ribosomal stalk protein P2 by chemical shift perturbation and mutagenesis analyses.
  Nucleic Acids Res, 35, 1660-1672.  
17621307 E.S.Poole, D.J.Young, M.E.Askarian-Amiri, D.J.Scarlett, and W.P.Tate (2007).
Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome.
  Cell Res, 17, 591-607.  
17324941 E.Torarinsson, J.H.Havgaard, and J.Gorodkin (2007).
Multiple structural alignment and clustering of RNA sequences.
  Bioinformatics, 23, 926-932.  
17651434 E.V.Ivanova, P.M.Kolosov, B.Birdsall, G.Kelly, A.Pastore, L.L.Kisselev, and V.I.Polshakov (2007).
Eukaryotic class 1 translation termination factor eRF1--the NMR structure and dynamics of the middle domain involved in triggering ribosome-dependent peptidyl-tRNA hydrolysis.
  FEBS J, 274, 4223-4237.
PDB code: 2hst
18041896 F.Franceschi (2007).
Back to the future: the ribosome as an antibiotic target.
  Future Microbiol, 2, 571-574.  
17048124 F.Leontiadou, A.Tsagkalia, and T.Choli-Papadopoulou (2007).
Thermus thermophilus L4 ribosomal protein: purification and sensitivity alteration against erythromycin of E. coli cells harboring a single amino acid mutant of TthL4 within its extended loop.
  Amino Acids, 33, 463-468.  
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.  
17688253 G.Todd, and K.Karbstein (2007).
RNA takes center stage.
  Biopolymers, 87, 275-278.  
17466623 H.Jin, J.P.Loria, and P.B.Moore (2007).
Solution structure of an rRNA substrate bound to the pseudouridylation pocket of a box H/ACA snoRNA.
  Mol Cell, 26, 205-215.
PDB codes: 2pcv 2pcw
17895397 H.Li, R.Liang, D.H.Turner, L.J.Rothberg, and S.Duan (2007).
Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure.
  RNA, 13, 2034-2041.  
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
17586759 H.S.Zaher, and P.J.Unrau (2007).
Selection of an improved RNA polymerase ribozyme with superior extension and fidelity.
  RNA, 13, 1017-1026.  
17186525 J.J.Ellis, M.Broom, and S.Jones (2007).
Protein-RNA interactions: structural analysis and functional classes.
  Proteins, 66, 903-911.  
17505105 J.Kondo, T.Sunami, and A.Takénaka (2007).
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.
  Acta Crystallogr D Biol Crystallogr, 63, 673-681.
PDB code: 2got
17245450 J.L.Baxter-Roshek, A.N.Petrov, and J.D.Dinman (2007).
Optimization of ribosome structure and function by rRNA base modification.
  PLoS ONE, 2, e174.  
17253975 J.Lacadena, E.Alvarez-García, N.Carreras-Sangrà, E.Herrero-Galán, J.Alegre-Cebollada, L.García-Ortega, M.Oñaderra, J.G.Gavilanes, and A.Martínez del Pozo (2007).
Fungal ribotoxins: molecular dissection of a family of natural killers.
  FEMS Microbiol Rev, 31, 212-237.  
17158708 J.Liu, and D.M.Lilley (2007).
The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA.
  RNA, 13, 200-210.  
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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17641824 J.Rinnenthal, C.Richter, J.Ferner, E.Duchardt, and H.Schwalbe (2007).
Quantitative gamma-HCNCH: determination of the glycosidic torsion angle chi in RNA oligonucleotides from the analysis of CH dipolar cross-correlated relaxation by solution NMR spectroscopy.
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17188006 J.S.Weinger, and S.A.Strobel (2007).
Exploring the mechanism of protein synthesis with modified substrates and novel intermediate mimics.
  Blood Cells Mol Dis, 38, 110-116.  
17449731 J.Zoll, M.Tessari, F.J.Van Kuppeveld, W.J.Melchers, and H.A.Heus (2007).
Breaking pseudo-twofold symmetry in the poliovirus 3'-UTR Y-stem by restoring Watson-Crick base pairs.
  RNA, 13, 781-792.
PDB codes: 2grw 2gv4
17636016 K.Caban, S.A.Kinzy, and P.R.Copeland (2007).
The L7Ae RNA binding motif is a multifunctional domain required for the ribosome-dependent Sec incorporation activity of Sec insertion sequence binding protein 2.
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17514744 K.Karbstein (2007).
Role of GTPases in ribosome assembly.
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17553838 K.Kitahara, A.Kajiura, N.S.Sato, and T.Suzuki (2007).
Functional genetic selection of Helix 66 in Escherichia coli 23S rRNA identified the eukaryotic-binding sequence for ribosomal protein L2.
  Nucleic Acids Res, 35, 4018-4029.  
17499045 K.L.Leach, S.M.Swaney, J.R.Colca, W.G.McDonald, J.R.Blinn, L.M.Thomasco, R.C.Gadwood, D.Shinabarger, L.Xiong, and A.S.Mankin (2007).
The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria.
  Mol Cell, 26, 393-402.  
17704156 K.Réblová, E.Fadrná, J.Sarzynska, T.Kulinski, P.Kulhánek, E.Ennifar, J.Koca, and J.Sponer (2007).
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.
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17210648 K.Shefer, Y.Brown, V.Gorkovoy, T.Nussbaum, N.B.Ulyanov, and Y.Tzfati (2007).
A triple helix within a pseudoknot is a conserved and essential element of telomerase RNA.
  Mol Cell Biol, 27, 2130-2143.  
17317683 K.St-Onge, P.Thibault, S.Hamel, and F.Major (2007).
Modeling RNA tertiary structure motifs by graph-grammars.
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17707400 L.M.Wadley, K.S.Keating, C.M.Duarte, and A.M.Pyle (2007).
Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure.
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17468242 L.Sojka, V.Fucík, L.Krásný, I.Barvík, and J.Jonák (2007).
YbxF, a protein associated with exponential-phase ribosomes in Bacillus subtilis.
  J Bacteriol, 189, 4809-4814.  
17685395 M.A.Ditzler, E.A.Alemán, D.Rueda, and N.G.Walter (2007).
Focus on function: single molecule RNA enzymology.
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17499039 M.Beringer, and M.V.Rodnina (2007).
The ribosomal peptidyl transferase.
  Mol Cell, 26, 311-321.