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PDBsum entry 1c04

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protein dna_rna links
Ribosome PDB id
1c04
Jmol
Contents
Protein chains
135 a.a. *
164 a.a. *
67 a.a. *
122 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1c04
Name: Ribosome
Title: Identification of known protein and RNA structures in a 5 a map of the large ribosomal subunit from haloarcula marismortui
Structure: 23s rrna fragment. Chain: e. Fragment: 23s rrna 1151-1208 region. Other_details: RNA e. Coli sequence and model. 23s rrna fragment. Chain: f. Fragment: 23s rrna helix 95. Other_details: RNA rat sequence and model. Ribosomal protein l2.
Source: Haloarcula marismortui. Organism_taxid: 2238. Organism_taxid: 2238
Biol. unit: Hexamer (from PQS)
Resolution:
5.00Å     R-factor:   not given    
Authors: N.Ban,P.Nissen,M.Capel,P.B.Moore,T.A.Steitz
Key ref:
N.Ban et al. (1999). Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit. Nature, 400, 841-847. PubMed id: 10476961 DOI: 10.1038/23641
Date:
14-Jul-99     Release date:   31-Aug-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04257  (RL2_GEOSE) -  50S ribosomal protein L2
Seq:
Struc:
276 a.a.
135 a.a.
Protein chain
No UniProt id for this chain
Struc: 164 a.a.
Protein chain
Pfam   ArchSchema ?
P14122  (RL11_HALMA) -  50S ribosomal protein L11
Seq:
Struc:
162 a.a.
67 a.a.*
Protein chain
Pfam   ArchSchema ?
P22450  (RL14_HALMA) -  50S ribosomal protein L14
Seq:
Struc:
132 a.a.
122 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 111 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   3 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     4 terms  

 

 
DOI no: 10.1038/23641 Nature 400:841-847 (1999)
PubMed id: 10476961  
 
 
Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit.
N.Ban, P.Nissen, J.Hansen, M.Capel, P.B.Moore, T.A.Steitz.
 
  ABSTRACT  
 
We have calculated at 5.0 A resolution an electron-density map of the large 50S ribosomal subunit from the bacterium Haloarcula marismortui by using phases derived from four heavy-atom derivatives, intercrystal density averaging and density-modification procedures. More than 300 base pairs of A-form RNA duplex have been fitted into this map, as have regions of non-A-form duplex, single-stranded segments and tetraloops. The long rods of RNA crisscrossing the subunit arise from the stacking of short, separate double helices, not all of which are A-form, and in many places proteins crosslink two or more of these rods. The polypeptide exit channel was marked by tungsten cluster compounds bound in one heavy-atom-derivatized crystal. We have determined the structure of the translation-factor-binding centre by fitting the crystal structures of the ribosomal proteins L6, L11 and L14, the sarcin-ricin loop RNA, and the RNA sequence that binds L11 into the electron density. We can position either elongation factor G or elongation factor Tu complexed with an aminoacylated transfer RNA and GTP onto the factor-binding centre in a manner that is consistent with results from biochemical and electron microscopy studies.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Visualization of the tunnel in which tungsten clusters are located. a, Stereo view, rotated by 90° about the vertical axis from the crown view (Fig. 1b, c) and showing the four tungsten clusters that mark the polypeptide exit tunnel. b, Close-up fo the tunnel sliced on one side to show the four tungsten clusters. The surface is gold on the outside and blue on the inside and represents the low electron density (empty space) in the proximity of the clusters.
Figure 4.
Figure 4 The fitting of previously solved protein and nucleic acid structures to the 5Å-resolution electron density map. a, The known crystal structure of a protein L2 fragment36 and an unknown -helical protein are seen to be interacting with an RNA helix that forms the base of a stalk on which protein L1 (not shown) sits. b, Crystal structure of the protein L11 C-terminal domain complexed with 58 nucleotides of rRNA^20,21 fitted into the electron density. c, The crystal structures of protein L6 (ref. 29) and the sarcin-ricin loop16,17, as well as two other RNA regions are fitted into density. d, The density identified as the SRL shows the characteristic S-turn in the RNA backbone. Proteins L14 (ref. 34) and L6 are seen to interact with the SRL on opposite sides.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 400, 841-847) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23385464 S.O.Dahms, M.Kuester, C.Streb, C.Roth, N.Sträter, and M.E.Than (2013).
Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 69, 284-297.  
21151115 I.G.Muñoz, H.Yébenes, M.Zhou, P.Mesa, M.Serna, A.Y.Park, E.Bragado-Nilsson, A.Beloso, G.de Cárcer, M.Malumbres, C.V.Robinson, J.M.Valpuesta, and G.Montoya (2011).
Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin.
  Nat Struct Mol Biol, 18, 14-19.
PDB code: 2xsm
20382999 A.J.McCoy, and R.J.Read (2010).
Experimental phasing: best practice and pitfalls.
  Acta Crystallogr D Biol Crystallogr, 66, 458-469.  
20179343 B.P.Pedersen, J.P.Morth, and P.Nissen (2010).
Structure determination using poorly diffracting membrane-protein crystals: the H+-ATPase and Na+,K+-ATPase case history.
  Acta Crystallogr D Biol Crystallogr, 66, 309-313.  
20974910 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
  Proc Natl Acad Sci U S A, 107, 19754-19759.
PDB codes: 3iz5 3iz6 3iz7 3iz9 3izr
20980660 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
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
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
  HFSP J, 4, 109-121.  
20358253 R.Sabate, N.S.de Groot, and S.Ventura (2010).
Protein folding and aggregation in bacteria.
  Cell Mol Life Sci, 67, 2695-2715.  
20127083 Y.Wei, and S.Daunert (2010).
Enabling technologies in discovery: the 2009 Nobel Prize and its implications in antibiotic design.
  Anal Bioanal Chem, 396, 1623-1626.  
19171966 A.M.Karmali, T.L.Blundell, and N.Furnham (2009).
Model-building strategies for low-resolution X-ray crystallographic data.
  Acta Crystallogr D Biol Crystallogr, 65, 121-127.  
19604473 C.Oubridge, D.A.Krummel, A.K.Leung, J.Li, and K.Nagai (2009).
Interpreting a low resolution map of human U1 snRNP using anomalous scatterers.
  Structure, 17, 930-938.  
19492077 C.Zhang, and A.Kuspa (2009).
Transcriptional down-regulation and rRNA cleavage in Dictyostelium discoideum mitochondria during Legionella pneumophila infection.
  PLoS One, 4, e5706.  
19325628 D.A.Pomeranz Krummel, C.Oubridge, A.K.Leung, J.Li, and K.Nagai (2009).
Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.
  Nature, 458, 475-480.
PDB code: 3cw1
19307722 D.Hamdane, C.Lechauve, M.C.Marden, and B.Golinelli-Pimpaneau (2009).
Pseudo-merohedral twinning in monoclinic crystals of wild-type human brain neuroglobin.
  Acta Crystallogr D Biol Crystallogr, 65, 388-392.  
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.  
19204001 L.N.Dimitrova, K.Kuroha, T.Tatematsu, and T.Inada (2009).
Nascent Peptide-dependent Translation Arrest Leads to Not4p-mediated Protein Degradation by the Proteasome.
  J Biol Chem, 284, 10343-10352.  
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.  
19938030 M.Sprinzl, and V.A.Erdmann (2009).
Protein biosynthesis on ribosomes in molecular resolution: nobel prize for chemistry 2009 goes to three chemical biologists.
  Chembiochem, 10, 2851-2853.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
19171964 S.Jenni, and N.Ban (2009).
Imperfect pseudo-merohedral twinning in crystals of fungal fatty acid synthase.
  Acta Crystallogr D Biol Crystallogr, 65, 101-111.  
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
  19054741 A.Ciammaruconi, S.Gorini, and P.Londei (2008).
A bifunctional archaeal protein that is a component of 30S ribosomal subunits and interacts with C/D box small RNAs.
  Archaea, 2, 151-158.  
18310328 D.Samanta, D.Mukhopadhyay, S.Chowdhury, J.Ghosh, S.Pal, A.Basu, A.Bhattacharya, A.Das, D.Das, and C.DasGupta (2008).
Protein folding by domain V of Escherichia coli 23S rRNA: specificity of RNA-protein interactions.
  J Bacteriol, 190, 3344-3352.  
17242508 A.Sultana, I.Alexeev, I.Kursula, P.Mäntsälä, J.Niemi, and G.Schneider (2007).
Structure determination by multiwavelength anomalous diffraction of aclacinomycin oxidoreductase: indications of multidomain pseudomerohedral twinning.
  Acta Crystallogr D Biol Crystallogr, 63, 149-159.
PDB code: 2ipi
17505114 J.G.Wittmann, and M.G.Rudolph (2007).
Pseudo-merohedral twinning in monoclinic crystals of human orotidine-5'-monophosphate decarboxylase.
  Acta Crystallogr D Biol Crystallogr, 63, 744-749.  
17468501 S.Smit, J.Widmann, and R.Knight (2007).
Evolutionary rates vary among rRNA structural elements.
  Nucleic Acids Res, 35, 3339-3354.  
17173023 W.C.Merrick (2007).
Are we there yet?
  Nat Chem Biol, 3, 19-20.  
16540469 J.Dresios, Y.L.Chan, and I.G.Wool (2006).
Determination of the amino acids in yeast ribosomal protein YS11 essential for the recognition of nucleotides in 18 S ribosomal RNA.
  J Biol Chem, 281, 13478-13484.  
16765890 P.A.Meyer, P.Ye, M.Zhang, M.H.Suh, and J.Fu (2006).
Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model.
  Structure, 14, 973-982.
PDB code: 2b8k
15978067 E.Evguenieva-Hackenberg (2005).
Bacterial ribosomal RNA in pieces.
  Mol Microbiol, 57, 318-325.  
15952884 J.M.Ogle, and V.Ramakrishnan (2005).
Structural insights into translational fidelity.
  Annu Rev Biochem, 74, 129-177.  
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Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila.
  Genes Cells, 10, 1163-1173.  
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Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction.
  Mol Cell, 20, 437-448.
PDB codes: 1vq4 1vq5 1vq8 1vq9 1vqk 1vql 1vqm 1vqo 1vqp
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Altered glucose metabolism and proteolysis in pancreatic cancer cell conditioned myoblasts: searching for a gene expression pattern with a microarray analysis of 5000 skeletal muscle genes.
  Gut, 53, 1159-1166.  
15039553 M.G.Rudolph, C.Wingren, M.P.Crowley, Y.H.Chien, and I.A.Wilson (2004).
Combined pseudo-merohedral twinning, non-crystallographic symmetry and pseudo-translation in a monoclinic crystal form of the gammadelta T-cell ligand T10.
  Acta Crystallogr D Biol Crystallogr, 60, 656-664.
PDB code: 1r3h
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.
  Mol Cell, 14, 57-66.  
15112238 W.P.Tate, and E.S.Poole (2004).
The ribosome: lifting the veil from a fascinating organelle.
  Bioessays, 26, 582-588.  
14627814 C.C.Correll, J.Beneken, M.J.Plantinga, M.Lubbers, and Y.L.Chan (2003).
The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure.
  Nucleic Acids Res, 31, 6806-6818.
PDB codes: 1q93 1q96 1q9a
12409297 C.L.Hanson, P.Fucini, L.L.Ilag, K.H.Nierhaus, and C.V.Robinson (2003).
Dissociation of intact Escherichia coli ribosomes in a mass spectrometer. Evidence for conformational change in a ribosome elongation factor G complex.
  J Biol Chem, 278, 1259-1267.  
12823544 H.Niwa, A.G.Tonevitsky, I.I.Agapov, S.Saward, U.Pfüller, and R.A.Palmer (2003).
Crystal structure at 3 A of mistletoe lectin I, a dimeric type-II ribosome-inactivating protein, complexed with galactose.
  Eur J Biochem, 270, 2739-2749.
PDB code: 1oql
13130133 J.M.Zengel, A.Jerauld, A.Walker, M.C.Wahl, and L.Lindahl (2003).
The extended loops of ribosomal proteins L4 and L22 are not required for ribosome assembly or L4-mediated autogenous control.
  RNA, 9, 1188-1197.  
12554939 M.G.Rudolph, M.S.Kelker, T.R.Schneider, T.O.Yeates, V.Oseroff, D.K.Heidary, P.A.Jennings, and I.A.Wilson (2003).
Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta.
  Acta Crystallogr D Biol Crystallogr, 59, 290-298.
PDB code: 1l2h
14527328 P.B.Moore, and T.A.Steitz (2003).
The structural basis of large ribosomal subunit function.
  Annu Rev Biochem, 72, 813-850.  
12620867 S.Behrens, C.Rühland, J.Inácio, H.Huber, A.Fonseca, I.Spencer-Martins, B.M.Fuchs, and R.Amann (2003).
In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes.
  Appl Environ Microbiol, 69, 1748-1758.  
12869707 S.Marzi, W.Knight, L.Brandi, E.Caserta, N.Soboleva, W.E.Hill, C.O.Gualerzi, and J.S.Lodmell (2003).
Ribosomal localization of translation initiation factor IF2.
  RNA, 9, 958-969.  
11976489 A.Royant, S.Grizot, R.Kahn, H.Belrhali, F.Fieschi, E.M.Landau, and E.Pebay-Peyroula (2002).
Detection and characterization of merohedral twinning in two protein crystals: bacteriorhodopsin and p67(phox).
  Acta Crystallogr D Biol Crystallogr, 58, 784-791.  
11988470 A.Yonath (2002).
The search and its outcome: high-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states.
  Annu Rev Biophys Biomol Struct, 31, 257-273.  
12202495 C.Gueydan, C.Wauquier, C.De Mees, G.Huez, and V.Kruys (2002).
Identification of ribosomal proteins specific to higher eukaryotic organisms.
  J Biol Chem, 277, 45034-45040.  
12490711 J.M.Zimmerman, and L.J.Maher (2002).
In vivo selection of spectinomycin-binding RNAs.
  Nucleic Acids Res, 30, 5425-5435.  
12146982 L.Montoya-García, V.Muñoz-Ocotero, R.Aguilar, and E.Sánchez de Jiménez (2002).
Regulation of acidic ribosomal protein expression and phosphorylation in maize.
  Biochemistry, 41, 10166-10172.  
12454464 N.A.Larsen, A.Heine, P.de Prada, e.l.-.R.Redwan, T.O.Yeates, D.W.Landry, and I.A.Wilson (2002).
Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal.
  Acta Crystallogr D Biol Crystallogr, 58, 2055-2059.  
12037305 N.Nevskaya, S.Tishchenko, M.Paveliev, Y.Smolinskaya, R.Fedorov, W.Piendl, Y.Nakamura, T.Toyoda, M.Garber, and S.Nikonov (2002).
Structure of ribosomal protein L1 from Methanococcus thermolithotrophicus. Functionally important structural invariants on the L1 surface.
  Acta Crystallogr D Biol Crystallogr, 58, 1023-1029.
PDB code: 1dwu
12162807 S.Miyata, K.Furuki, K.Oshima, T.Sawayanagi, H.Nishigawa, S.Kakizawa, H.Y.Jung, M.Ugaki, and S.Namba (2002).
Complete nucleotide sequence of the S10-spc operon of phytoplasma: gene organization and genetic code resemble those of Bacillus subtilis.
  DNA Cell Biol, 21, 527-534.  
12060678 T.Shimizu, M.Nakagaki, Y.Nishi, Y.Kobayashi, A.Hachimori, and T.Uchiumi (2002).
Interaction among silkworm ribosomal proteins P1, P2 and P0 required for functional protein binding to the GTPase-associated domain of 28S rRNA.
  Nucleic Acids Res, 30, 2620-2627.  
11729183 T.Uchiumi, S.Honma, T.Nomura, E.R.Dabbs, and A.Hachimori (2002).
Translation elongation by a hybrid ribosome in which proteins at the GTPase center of the Escherichia coli ribosome are replaced with rat counterparts.
  J Biol Chem, 277, 3857-3862.  
11849993 W.J.He, S.Tang, and W.Y.Liu (2002).
In vitro interaction of eukaryotic elongation factor 2 with synthetic oligoribonucleotide that mimics GTPase domain of rat 28S ribosomal RNA.
  Int J Biochem Cell Biol, 34, 263-268.  
12762007 A.Bashan, I.Agmon, R.Zarivach, F.Schluenzen, J.Harms, M.Pioletti, H.Bartels, M.Gluehmann, H.Hansen, T.Auerbach, F.Franceschi, and A.Yonath (2001).
High-resolution structures of ribosomal subunits: initiation, inhibition, and conformational variability.
  Cold Spring Harb Symp Quant Biol, 66, 43-56.  
11341947 A.Walles-Granberg, R.Schnell, L.A.Isaksson, and M.Rydén-Aulin (2001).
Ribosomes with large synthetic N-terminal extensions of protein S15 are active in vivo.
  Biochim Biophys Acta, 1544, 378-385.  
11120937 B.Vester, and S.Douthwaite (2001).
Macrolide resistance conferred by base substitutions in 23S rRNA.
  Antimicrob Agents Chemother, 45, 1.  
11389850 C.M.Spahn, G.Blaha, R.K.Agrawal, P.Penczek, R.A.Grassucci, C.A.Trieber, S.R.Connell, D.E.Taylor, K.H.Nierhaus, and J.Frank (2001).
Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance.
  Mol Cell, 7, 1037-1045.  
11828423 D.M.Lilley (2001).
The ribosome functions as a ribozyme.
  Chembiochem, 2, 31-35.  
11441810 E.A.Doherty, and J.A.Doudna (2001).
Ribozyme structures and mechanisms.
  Annu Rev Biophys Biomol Struct, 30, 457-475.  
11209054 E.A.Gaucher, M.M.Miyamoto, and S.A.Benner (2001).
Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors.
  Proc Natl Acad Sci U S A, 98, 548-552.  
11406375 F.Major, and R.Griffey (2001).
Computational methods for RNA structure determination.
  Curr Opin Struct Biol, 11, 282-286.  
12762045 G.R.Andersen, and J.Nyborg (2001).
Structural studies of eukaryotic elongation factors.
  Cold Spring Harb Symp Quant Biol, 66, 425-437.  
11494321 J.Frank (2001).
Cryo-electron microscopy as an investigative tool: the ribosome as an example.
  Bioessays, 23, 725-732.  
12762006 J.L.Hansen, T.M.Schmeing, D.J.Klein, J.A.Ippolito, N.Ban, P.Nissen, B.Freeborn, P.B.Moore, and T.A.Steitz (2001).
Progress toward an understanding of the structure and enzymatic mechanism of the large ribosomal subunit.
  Cold Spring Harb Symp Quant Biol, 66, 33-42.  
11168361 M.C.Kiel, and M.C.Ganoza (2001).
Functional interactions of an Escherichia coli ribosomal ATPase.
  Eur J Biochem, 268, 278-286.  
11395413 M.V.Rodnina, and W.Wintermeyer (2001).
Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms.
  Annu Rev Biochem, 70, 415-435.  
11258942 P.B.Moore (2001).
The ribosome at atomic resolution.
  Biochemistry, 40, 3243-3250.  
11532164 P.Pesaresi, C.Varotto, J.Meurer, P.Jahns, F.Salamini, and D.Leister (2001).
Knock-out of the plastid ribosomal protein L11 in Arabidopsis: effects on mRNA translation and photosynthesis.
  Plant J, 27, 179-189.  
11470155 R.Willumeit, G.Diedrich, S.Forthmann, J.Beckmann, R.P.May, H.B.Stuhrmann, and K.H.Nierhaus (2001).
Mapping proteins of the 50S subunit from Escherichia coli ribosomes.
  Biochim Biophys Acta, 1520, 7.  
11327859 T.Yoshida, S.Uchiyama, H.Nakano, H.Kashimori, H.Kijima, T.Ohshima, Y.Saihara, T.Ishino, H.Shimahara, T.Yoshida, K.Yokose, T.Ohkubo, A.Kaji, and Y.Kobayashi (2001).
Solution structure of the ribosome recycling factor from Aquifex aeolicus.
  Biochemistry, 40, 2387-2396.
PDB code: 1ge9
11297922 V.Ramakrishnan, and P.B.Moore (2001).
Atomic structures at last: the ribosome in 2000.
  Curr Opin Struct Biol, 11, 144-154.  
11340059 W.Wang, O.Donini, C.M.Reyes, and P.A.Kollman (2001).
Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.
  Annu Rev Biophys Biomol Struct, 30, 211-243.  
12762047 W.Wintermeyer, A.Savelsbergh, Y.P.Semenkov, V.I.Katunin, and M.V.Rodnina (2001).
Mechanism of elongation factor G function in tRNA translocation on the ribosome.
  Cold Spring Harb Symp Quant Biol, 66, 449-458.  
11160931 Y.M.Hou, X.Zhang, J.A.Holland, and D.R.Davis (2001).
An important 2'-OH group for an RNA-protein interaction.
  Nucleic Acids Res, 29, 976-985.  
10679466 A.A.Antson (2000).
Single-stranded-RNA binding proteins.
  Curr Opin Struct Biol, 10, 87-94.  
10805779 A.A.Rostom, P.Fucini, D.R.Benjamin, R.Juenemann, K.H.Nierhaus, F.U.Hartl, C.M.Dobson, and C.V.Robinson (2000).
Detection and selective dissociation of intact ribosomes in a mass spectrometer.
  Proc Natl Acad Sci U S A, 97, 5185-5190.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
10966462 A.J.Herr, J.F.Atkins, and R.F.Gesteland (2000).
Coupling of open reading frames by translational bypassing.
  Annu Rev Biochem, 69, 343-372.  
10836789 A.Satoh, K.Takai, R.Ouchi, S.Yokoyama, and H.Takaku (2000).
Effects of anticodon 2'-O-methylations on tRNA codon recognition in an Escherichia coli cell-free translation.
  RNA, 6, 680-686.  
10786831 B.Bukau, E.Deuerling, C.Pfund, and E.A.Craig (2000).
Getting newly synthesized proteins into shape.
  Cell, 101, 119-122.  
10919826 B.M.Fuchs, F.O.Glöckner, J.Wulf, and R.Amann (2000).
Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes.
  Appl Environ Microbiol, 66, 3603-3607.  
11071938 C.Briones, and J.P.Ballesta (2000).
Conformational changes induced in the Saccharomyces cerevisiae GTPase-associated rRNA by ribosomal stalk components and a translocation inhibitor.
  Nucleic Acids Res, 28, 4497-4505.  
10745014 C.Davies, and S.W.White (2000).
Electrons and X-rays gang up on the ribosome.
  Structure, 8, R41-R45.  
10986461 C.M.Spahn, P.A.Penczek, A.Leith, and J.Frank (2000).
A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome.
  Structure, 8, 937-948.  
10981630 C.R.Lowe (2000).
Nanobiotechnology: the fabrication and applications of chemical and biological nanostructures.
  Curr Opin Struct Biol, 10, 428-434.  
11188692 C.T.Farrar, J.Ma, D.J.Singel, and C.J.Halkides (2000).
Structural changes induced in p21Ras upon GAP-334 complexation as probed by ESEEM spectroscopy and molecular-dynamics simulation.
  Structure, 8, 1279-1287.  
10799526 D.I.Svergun, and K.H.Nierhaus (2000).
A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome.
  J Biol Chem, 275, 14432-14439.  
10880458 D.Mohr, W.Wintermeyer, and M.V.Rodnina (2000).
Arginines 29 and 59 of elongation factor G are important for GTP hydrolysis or translocation on the ribosome.
  EMBO J, 19, 3458-3464.  
10966470 E.A.Doherty, and J.A.Doudna (2000).
Ribozyme structures and mechanisms.
  Annu Rev Biochem, 69, 597-615.  
10944332 F.Yang, Z.Dauter, and A.Wlodawer (2000).
Effects of crystal twinning on the ability to solve a macromolecular structure using multiwavelength anomalous diffraction.
  Acta Crystallogr D Biol Crystallogr, 56, 959-964.  
11013226 G.Diedrich, C.M.Spahn, U.Stelzl, M.A.Schäfer, T.Wooten, D.E.Bochkariov, B.S.Cooperman, R.R.Traut, and K.H.Nierhaus (2000).
Ribosomal protein L2 is involved in the association of the ribosomal subunits, tRNA binding to A and P sites and peptidyl transfer.
  EMBO J, 19, 5241-5250.  
10981637 G.G.Shipley (2000).
Bilayers and nonbilayers: structure, forces and protein crystallization.
  Curr Opin Struct Biol, 10, 471-473.  
10747796 G.W.Muth, S.P.Hennelly, and W.E.Hill (2000).
Using a targeted chemical nuclease to elucidate conformational changes in the E. coli 30S ribosomal subunit.
  Biochemistry, 39, 4068-4074.  
10943895 H.Koosha, D.Cameron, K.Andrews, A.E.Dahlberg, and P.E.March (2000).
Alterations in the peptidyltransferase and decoding domains of ribosomal RNA suppress mutations in the elongation factor G gene.
  RNA, 6, 1166-1173.  
10676812 H.Stark, M.V.Rodnina, H.J.Wieden, M.van Heel, and W.Wintermeyer (2000).
Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation.
  Cell, 100, 301-309.  
10721991 I.S.Gabashvili, R.K.Agrawal, C.M.Spahn, R.A.Grassucci, D.I.Svergun, J.Frank, and P.Penczek (2000).
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
  Cell, 100, 537-549.
PDB code: 1eg0
10889033 J.A.Pleiss, A.D.Wolfson, and O.C.Uhlenbeck (2000).
Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA molecule.
  Biochemistry, 39, 8250-8258.  
11073222 J.Carnes, L.Frolova, S.Zinnen, G.Drugeon, M.Phillippe, J.Justesen, A.L.Haenni, L.Leinwand, L.L.Kisselev, and M.Yarus (2000).
Suppression of eukaryotic translation termination by selected RNAs.
  RNA, 6, 1468-1479.  
10852723 J.Dresios, I.L.Derkatch, S.W.Liebman, and D.Synetos (2000).
Yeast ribosomal protein L24 affects the kinetics of protein synthesis and ribosomal protein L39 improves translational accuracy, while mutants lacking both remain viable.
  Biochemistry, 39, 7236-7244.  
10671531 J.R.Hesselberth, D.Miller, J.Robertus, and A.D.Ellington (2000).
In vitro selection of RNA molecules that inhibit the activity of ricin A-chain.
  J Biol Chem, 275, 4937-4942.  
10968986 J.Sarzynska, T.Kulinski, and L.Nilsson (2000).
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
  Biophys J, 79, 1213-1227.  
10882112 J.Vilardell, S.J.Yu, and J.R.Warner (2000).
Multiple functions of an evolutionarily conserved RNA binding domain.
  Mol Cell, 5, 761-766.  
11095680 J.Wuyts, P.De Rijk, Y.Van de Peer, G.Pison, P.Rousseeuw, and R.De Wachter (2000).
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.
  Nucleic Acids Res, 28, 4698-4708.  
10811627 K.K.Kim, K.Min, and S.W.Suh (2000).
Crystal structure of the ribosome recycling factor from Escherichia coli.
  EMBO J, 19, 2362-2370.
PDB code: 1ek8
11154066 K.R.Katsani, P.Tsiboli, K.Anagnostopoulos, H.Urlaub, and T.Choli-Papadopoulou (2000).
Identification of the 50S ribosomal proteins from the Eubacterium Thermus thermophilus.
  Biol Chem, 381, 1079-1087.  
10986233 L.Xiong, P.Kloss, S.Douthwaite, N.M.Andersen, S.Swaney, D.L.Shinabarger, and A.S.Mankin (2000).
Oxazolidinone resistance mutations in 23S rRNA of Escherichia coli reveal the central region of domain V as the primary site of drug action.
  J Bacteriol, 182, 5325-5331.  
10637222 M.C.Wahl, G.P.Bourenkov, H.D.Bartunik, and R.Huber (2000).
Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12.
  EMBO J, 19, 174-186.
PDB codes: 1dd3 1dd4
10835368 M.G.Gomez-Lorenzo, C.M.Spahn, R.K.Agrawal, R.A.Grassucci, P.Penczek, K.Chakraburtty, J.P.Ballesta, J.L.Lavandera, J.F.Garcia-Bustos, and J.Frank (2000).
Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 A resolution.
  EMBO J, 19, 2710-2718.  
10998631 M.G.Rossmann (2000).
Fitting atomic models into electron-microscopy maps.
  Acta Crystallogr D Biol Crystallogr, 56, 1341-1349.  
10696113 M.Lu, and T.A.Steitz (2000).
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
  Proc Natl Acad Sci U S A, 97, 2023-2028.
PDB code: 1dfu
10937867 M.Sprinzl, S.Brock, Y.Huang, P.Milovnik, M.Nanninga, M.Nesper-Brock, H.Rütthard, and K.Szkaradkiewicz (2000).
Regulation of GTPases in the bacterial translation machinery.
  Biol Chem, 381, 367-375.  
10592212 M.Szymanski, M.Z.Barciszewska, J.Barciszewski, and V.A.Erdmann (2000).
5S ribosomal RNA database Y2K.
  Nucleic Acids Res, 28, 166-167.  
10937868 M.V.Rodnina, H.Stark, A.Savelsbergh, H.J.Wieden, D.Mohr, N.B.Matassova, F.Peske, T.Daviter, C.O.Gualerzi, and W.Wintermeyer (2000).
GTPases mechanisms and functions of translation factors on the ribosome.
  Biol Chem, 381, 377-387.  
10771437 M.Worbs, and M.C.Wahl (2000).
Expression, purification, crystallization and preliminary X-ray diffraction studies of bacterial and archaeal L4 ribosomal proteins.
  Acta Crystallogr D Biol Crystallogr, 56, 645-647.  
10698923 M.Worbs, R.Huber, and M.C.Wahl (2000).
Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon.
  EMBO J, 19, 807-818.
PDB code: 1dmg
10937989 N.Ban, P.Nissen, J.Hansen, P.B.Moore, and T.A.Steitz (2000).
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
  Science, 289, 905-920.
PDB code: 1ffk
10801481 N.Nevskaya, S.Tischenko, R.Fedorov, S.Al-Karadaghi, A.Liljas, A.Kraft, W.Piendl, M.Garber, and S.Nikonov (2000).
Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family.
  Structure, 8, 363-371.
PDB code: 1cjs
10949037 N.Polacek, S.Patzke, K.H.Nierhaus, and A.Barta (2000).
Periodic conformational changes in rRNA: monitoring the dynamics of translating ribosomes.
  Mol Cell, 6, 159-171.  
11004163 N.S.Chernyaeva, and E.J.Murgola (2000).
Covariance of complementary rRNA loop nucleotides does not necessarily represent functional pseudoknot formation in vivo.
  J Bacteriol, 182, 5671-5675.  
10677222 O.Piepenburg, T.Pape, J.A.Pleiss, W.Wintermeyer, O.C.Uhlenbeck, and M.V.Rodnina (2000).
Intact aminoacyl-tRNA is required to trigger GTP hydrolysis by elongation factor Tu on the ribosome.
  Biochemistry, 39, 1734-1738.  
10997906 P.Allard, A.V.Rak, B.T.Wimberly, W.M.Clemons, A.Kalinin, M.Helgstrand, M.B.Garber, V.Ramakrishnan, and T.Härd (2000).
Another piece of the ribosome: solution structure of S16 and its location in the 30S subunit.
  Structure, 8, 875-882.
PDB code: 1emw
10675317 P.Nissen, M.Kjeldgaard, and J.Nyborg (2000).
Macromolecular mimicry.
  EMBO J, 19, 489-495.  
11080632 R.Brimacombe (2000).
The bacterial ribosome at atomic resolution.
  Structure, 8, R195-R200.  
10837219 R.Green (2000).
Ribosomal translocation: EF-G turns the crank.
  Curr Biol, 10, R369-R373.  
11073218 R.Klinck, E.Westhof, S.Walker, M.Afshar, A.Collier, and F.Aboul-Ela (2000).
A potential RNA drug target in the hepatitis C virus internal ribosomal entry site.
  RNA, 6, 1423-1431.
PDB code: 1fqz
10679458 S.Blanquet, Y.Mechulam, and E.Schmitt (2000).
The many routes of bacterial transfer RNAs after aminoacylation.
  Curr Opin Struct Biol, 10, 95.  
10753109 S.C.Agalarov, G.Sridhar Prasad, P.M.Funke, C.D.Stout, and J.R.Williamson (2000).
Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain.
  Science, 288, 107-113.
PDB codes: 1ekc 1g1x
11114498 S.Chandra Sanyal, and A.Liljas (2000).
The end of the beginning: structural studies of ribosomal proteins.
  Curr Opin Struct Biol, 10, 633-636.  
10760175 S.Douthwaite, L.H.Hansen, and P.Mauvais (2000).
Macrolide-ketolide inhibition of MLS-resistant ribosomes is improved by alternative drug interaction with domain II of 23S rRNA.
  Mol Microbiol, 36, 183-193.  
10745015 T.Hermann, and D.J.Patel (2000).
RNA bulges as architectural and recognition motifs.
  Structure, 8, R47-R54.  
10781065 U.Stelzl, C.M.Spahn, and K.H.Nierhaus (2000).
Selecting rRNA binding sites for the ribosomal proteins L4 and L6 from randomly fragmented rRNA: application of a method called SERF.
  Proc Natl Acad Sci U S A, 97, 4597-4602.  
10787170 V.I.Zannis, and J.Cohen (2000).
Old and new players in the lipoprotein system.
  Curr Opin Lipidol, 11, 101-103.  
11050428 W.C.Lathe, B.Snel, and P.Bork (2000).
Gene context conservation of a higher order than operons.
  Trends Biochem Sci, 25, 474-479.  
11016950 W.V.Ng, S.P.Kennedy, G.G.Mahairas, B.Berquist, M.Pan, H.D.Shukla, S.R.Lasky, N.S.Baliga, V.Thorsson, J.Sbrogna, S.Swartzell, D.Weir, J.Hall, T.A.Dahl, R.Welti, Y.A.Goo, B.Leithauser, K.Keller, R.Cruz, M.J.Danson, D.W.Hough, D.G.Maddocks, P.E.Jablonski, M.P.Krebs, C.M.Angevine, H.Dale, T.A.Isenbarger, R.F.Peck, M.Pohlschroder, J.L.Spudich, K.W.Jung, M.Alam, T.Freitas, S.Hou, C.J.Daniels, P.P.Dennis, A.D.Omer, H.Ebhardt, T.M.Lowe, P.Liang, M.Riley, L.Hood, and S.DasSarma (2000).
Genome sequence of Halobacterium species NRC-1.
  Proc Natl Acad Sci U S A, 97, 12176-12181.  
10969026 W.Wriggers, R.K.Agrawal, D.L.Drew, A.McCammon, and J.Frank (2000).
Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures.
  Biophys J, 79, 1670-1678.  
10579710 A.Verschoor, and T.Lithgow (1999).
A first glimpse at the structure of the TOM translocase from the mitochondrial outer membrane.
  J Cell Biol, 147, 905-908.  
10647187 C.M.Spahn, R.A.Grassucci, P.Penczek, and J.Frank (1999).
Direct three-dimensional localization and positive identification of RNA helices within the ribosome by means of genetic tagging and cryo-electron microscopy.
  Structure, 7, 1567-1573.  
10619032 D.F.Kim, and R.Green (1999).
Base-pairing between 23S rRNA and tRNA in the ribosomal A site.
  Mol Cell, 4, 859-864.  
10562562 I.S.Gabashvili, R.K.Agrawal, R.Grassucci, C.L.Squires, A.E.Dahlberg, and J.Frank (1999).
Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA.
  EMBO J, 18, 6501-6507.  
10530999 J.A.Doudna (1999).
Cashing in on crystals.
  Curr Biol, 9, R731-R734.  
10647188 R.Matadeen, A.Patwardhan, B.Gowen, E.V.Orlova, T.Pape, M.Cuff, F.Mueller, R.Brimacombe, and M.van Heel (1999).
The Escherichia coli large ribosomal subunit at 7.5 A resolution.
  Structure, 7, 1575-1583.  
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