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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
1fka
Jmol
Contents
Protein chains
111 a.a.*
176 a.a.*
161 a.a. *
157 a.a. *
97 a.a. *
128 a.a. *
136 a.a. *
89 a.a.* *
70 a.a.* *
103 a.a.* *
77 a.a.* *
26 a.a.* *
88 a.a. *
84 a.a. *
50 a.a. *
73 a.a. *
95 a.a. *
DNA/RNA
Metals
WO2 ×7
* Residue conservation analysis
* C-alpha coords only
PDB id:
1fka
Name: Ribosome
Title: Structure of functionally activated small ribosomal subunit at 3.3 a resolution
Structure: 16s ribosomal RNA. Chain: a. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.
Source: Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
Biol. unit: 20mer (from PQS)
Resolution:
3.30Å     R-factor:   0.304     R-free:   0.305
Authors: F.Schluenzen,A.Tocilj,R.Zarivach,J.Harms,M.Gluehmann, D.Janell,A.Bashan,H.Bartels,I.Agmon,F.Franceschi,A.Yonath
Key ref:
F.Schluenzen et al. (2000). Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell, 102, 615-623. PubMed id: 11007480 DOI: 10.1016/S0092-8674(00)00084-2
Date:
09-Aug-00     Release date:   04-Sep-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Protein chain
No UniProt id for this chain
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  30S ribosomal protein S4
Seq:
Struc: 		209 a.a.
161 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5
Seq:
Struc: 		162 a.a.
157 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6
Seq:
Struc: 		101 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc: 		156 a.a.
128 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8
Seq:
Struc: 		138 a.a.
136 a.a.
Protein chain
No UniProt id for this chain
Protein chain
No UniProt id for this chain
Protein chain
No UniProt id for this chain
Protein chain
No UniProt id for this chain
Protein chain
No UniProt id for this chain
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15
Seq:
Struc: 		89 a.a.
88 a.a.*
Protein chain
No UniProt id for this chain
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18
Seq:
Struc: 		88 a.a.
50 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  30S ribosomal protein S19
Seq:
Struc: 		93 a.a.
73 a.a.
Protein chain
No UniProt id for this chain
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(00)00084-2 Cell 102:615-623 (2000)
PubMed id: 11007480  
 
 
Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.
F.Schluenzen, A.Tocilj, R.Zarivach, J.Harms, M.Gluehmann, D.Janell, A.Bashan, H.Bartels, I.Agmon, F.Franceschi, A.Yonath.
 
  ABSTRACT  
 
The small ribosomal subunit performs the decoding of genetic information during translation. The structure of that from Thermus thermophilus shows that the decoding center, which positions mRNA and three tRNAs, is constructed entirely of RNA. The entrance to the mRNA channel will encircle the message when a latch-like contact closes and contributes to processivity and fidelity. Extended RNA helical elements that run longitudinally through the body transmit structural changes, correlating events at the particle's far end with the cycle of mRNA translocation at the decoding region. 96% of the nucleotides were traced and the main fold of all proteins was determined. The latter are either peripheral or appear to serve as linkers. Some may assist the directionality of translocation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Small Subunit and Its Electron Density Map(Left and center) A stereo representation of the full model described in this paper. RNA is shown in gold, using a ribbon backbone and simple lines for base pairs. The differently colored helical segments and loops are the proteins. The major subdivisions are labeled: H, head; B, body; S, shoulder; P, platform; N, nose; F, foot.In all figures, the head is at the top of the drawing and the foot at the bottom.These portions of Figure 1 Figure 2 Figure 3 were made with Ribbons ( [12]).(Right) Segments showing RNA (top and middle pannels) and proteins (bottom) of the MIRAS map at 3.3 Å resolution, with the model superimposed. Made with O ([32]). 		Figure 3.
Figure 3. The Presumed mRNA Path(Left) A surface representation of the subunit, viewed from the side of the 50S subunit. The latch is circled in cyan and the decoding center in red. The mRNA would enter the path in the approximate direction shown by the dark-blue arrow, pass through the aperture defined by the latch, and along the channel in the near face of the subunit. The brown curved arrows show the suggested global cooperative movements of the platform and the head, which facilitate the mRNA entrance, progression, and exit.(Right) Enlarged image of the decoding center region, showing the positions of tRNA anticodon stem loops and mRNA codons, using the superposition of tRNA and mRNA from the model of Cate et al., 1999, as described in the text. The uppermost bulge of H44 is shown in olive, two codons of mRNA in blue, and the anticodon bases of the tRNA molecules in green (A site), magenta (P site) and gray (E site). The right side of the figure was made with DINO ([47]). The contour level is 1.1 standard deviations.
 
  The above figures are reprinted by permission from Cell Press: Cell (2000, 102, 615-623) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

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PDB code: 3iin
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PDB code: 3imq
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PDB codes: 3iz5 3iz6 3iz7 3iz9 3izr
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PDB codes: 3bbd 3bbe 3bbh
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Cooperativity in macromolecular assembly.
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RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
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Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation.
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Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases.
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Structure of the mammalian 80S ribosome at 8.7 A resolution.
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PDB codes: 2zkq 2zkr
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PDB code: 2jr0
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rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance.
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PDB codes: 3d3b 3d3c
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L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
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PDB codes: 2jq7 2nyo
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G-ribo: a new structural motif in ribosomal RNA.
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G-ribo motif favors the formation of pseudoknots in ribosomal RNA.
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A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.
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PDB code: 2e5l
17652406 V.Lisi, and F.Major (2007).
A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships.
  RNA, 13, 1537-1545.  
17203977 W.E.Running, S.Ravipaty, J.A.Karty, and J.P.Reilly (2007).
A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus.
  J Proteome Res, 6, 337-347.  
16855312 A.Liljas (2006).
On the complementarity of methods in structural biology.
  Acta Crystallogr D Biol Crystallogr, 62, 941-945.  
16556933 A.Pulk, U.Maiväli, and J.Remme (2006).
Identification of nucleotides in E. coli 16S rRNA essential for ribosome subunit association.
  RNA, 12, 790-796.  
16632247 C.A.Townsend, J.M.Crawford, and T.Bililign (2006).
New images evoke FAScinating questions.
  Chem Biol, 13, 349-351.  
16711863 C.Y.Lee (2006).
Mass fractal dimension of the ribosome and implication of its dynamic characteristics.
  Phys Rev E Stat Nonlin Soft Matter Phys, 73, 042901.  
16490268 E.C.Böttger (2006).
The ribosome as a drug target.
  Trends Biotechnol, 24, 145-147.  
16998488 F.Schluenzen, C.Takemoto, D.N.Wilson, T.Kaminishi, J.M.Harms, K.Hanawa-Suetsugu, W.Szaflarski, M.Kawazoe, M.Shirouzu, M.Shirouzo, K.H.Nierhaus, S.Yokoyama, and P.Fucini (2006).
The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation.
  Nat Struct Mol Biol, 13, 871-878.
PDB code: 2hhh
16773394 G.Papadopoulos, S.Grudinin, D.L.Kalpaxis, and T.Choli-Papadopoulou (2006).
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis.
  Eur Biophys J, 35, 675-683.  
16371706 G.Rosenbaum, R.W.Alkire, G.Evans, F.J.Rotella, K.Lazarski, R.G.Zhang, S.L.Ginell, N.Duke, I.Naday, J.Lazarz, M.J.Molitsky, L.Keefe, J.Gonczy, L.Rock, R.Sanishvili, M.A.Walsh, E.Westbrook, and A.Joachimiak (2006).
The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.
  J Synchrotron Radiat, 13, 30-45.  
17051149 G.Yusupova, L.Jenner, B.Rees, D.Moras, and M.Yusupov (2006).
Structural basis for messenger RNA movement on the ribosome.
  Nature, 444, 391-394.
PDB codes: 2hgi 2hgj 2hgp 2hgq 2hgr 2hgu
16717405 H.Yoneyama, and R.Katsumata (2006).
Antibiotic resistance in bacteria and its future for novel antibiotic development.
  Biosci Biotechnol Biochem, 70, 1060-1075.  
16553873 J.Dresios, P.Panopoulos, and D.Synetos (2006).
Eukaryotic ribosomal proteins lacking a eubacterial counterpart: important players in ribosomal function.
  Mol Microbiol, 59, 1651-1663.  
17069639 J.J.Gillespie, J.S.Johnston, J.J.Cannone, and R.R.Gutell (2006).
Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements.
  Insect Mol Biol, 15, 657-686.  
16276528 J.M.Chandonia, S.H.Kim, and S.E.Brenner (2006).
Target selection and deselection at the Berkeley Structural Genomics Center.
  Proteins, 62, 356-370.  
16778356 K.Koga, A.Ikegami, K.Nakasone, R.Murayama, G.Akanuma, Y.Natori, H.Nanamiya, and F.Kawamura (2006).
Construction of Bacillus subtilis strains carrying the transcriptional bgaB fusion with the promoter region of each rrn operon and their differential transcription during spore development.
  J Gen Appl Microbiol, 52, 119-124.  
16689638 K.Mitra, and J.Frank (2006).
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.
  Annu Rev Biophys Biomol Struct, 35, 299-317.  
16522648 L.Nasalean, S.Baudrey, N.B.Leontis, and L.Jaeger (2006).
Controlling RNA self-assembly to form filaments.
  Nucleic Acids Res, 34, 1381-1392.  
16721597 M.Buchhaupt, B.Meyer, P.Kötter, and K.D.Entian (2006).
Genetic evidence for 18S rRNA binding and an Rps19p assembly function of yeast nucleolar protein Nep1p.
  Mol Genet Genomics, 276, 273-284.  
17060325 M.G.Gagnon, A.Mukhopadhyay, and S.V.Steinberg (2006).
Close packing of helices 3 and 12 of 16 S rRNA is required for the normal ribosome function.
  J Biol Chem, 281, 39349-39357.  
16500956 M.Newby Lambert, E.Vöcker, S.Blumberg, S.Redemann, A.Gajraj, J.C.Meiners, and N.G.Walter (2006).
Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy.
  Biophys J, 90, 3672-3685.  
17005277 T.L.Sorensen, K.E.McAuley, R.Flaig, and E.M.Duke (2006).
New light for science: synchrotron radiation in structural medicine.
  Trends Biotechnol, 24, 500-508.  
16894217 W.J.Melchers, J.Zoll, M.Tessari, D.V.Bakhmutov, A.P.Gmyl, V.I.Agol, and H.A.Heus (2006).
A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA.
  RNA, 12, 1671-1682.
PDB code: 2evy
16199764 A.K.Woźniak, S.Nottrott, E.Kühn-Hölsken, G.F.Schröder, H.Grubmüller, R.Lührmann, C.A.Seidel, and F.Oesterhelt (2005).
Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements.
  RNA, 11, 1545-1554.  
  16511038 A.Matte, G.V.Louie, J.Sivaraman, M.Cygler, and S.K.Burley (2005).
Structure of the pseudouridine synthase RsuA from Haemophilus influenzae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 350-354.
PDB code: 1vio
16269538 A.Yassin, K.Fredrick, and A.S.Mankin (2005).
Deleterious mutations in small subunit ribosomal RNA identify functional sites and potential targets for antibiotics.
  Proc Natl Acad Sci U S A, 102, 16620-16625.  
16180279 A.Yonath (2005).
Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation.
  Annu Rev Biochem, 74, 649-679.  
15755955 B.S.Laursen, H.P.Sørensen, K.K.Mortensen, and H.U.Sperling-Petersen (2005).
Initiation of protein synthesis in bacteria.
  Microbiol Mol Biol Rev, 69, 101-123.  
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
15853795 D.E.Brodersen, and P.Nissen (2005).
The social life of ribosomal proteins.
  FEBS J, 272, 2098-2108.  
16336118 D.N.Wilson, J.M.Harms, K.H.Nierhaus, F.Schlünzen, and P.Fucini (2005).
Species-specific antibiotic-ribosome interactions: implications for drug development.
  Biol Chem, 386, 1239-1252.  
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.
  RNA, 11, 906-913.  
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.
  Biophys J, 88, 3466-3485.  
16141058 H.F.Noller (2005).
RNA structure: reading the ribosome.
  Science, 309, 1508-1514.  
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.  
16164408 I.Agmon, A.Bashan, R.Zarivach, and A.Yonath (2005).
Symmetry at the active site of the ribosome: structural and functional implications.
  Biol Chem, 386, 833-844.  
16111914 J.A.Sutcliffe (2005).
Improving on nature: antibiotics that target the ribosome.
  Curr Opin Microbiol, 8, 534-542.  
16313563 J.J.Gillespie, C.H.McKenna, M.J.Yoder, R.R.Gutell, J.S.Johnston, J.Kathirithamby, and A.I.Cognato (2005).
Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera).
  Insect Mol Biol, 14, 625-643.  
15952884 J.M.Ogle, and V.Ramakrishnan (2005).
Structural insights into translational fidelity.
  Annu Rev Biochem, 74, 129-177.  
16261170 J.Poehlsgaard, and S.Douthwaite (2005).
The bacterial ribosome as a target for antibiotics.
  Nat Rev Microbiol, 3, 870-881.  
15923259 L.L.Ilag, H.Videler, A.R.McKay, F.Sobott, P.Fucini, K.H.Nierhaus, and C.V.Robinson (2005).
Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria.
  Proc Natl Acad Sci U S A, 102, 8192-8197.  
15647501 M.Dorywalska, S.C.Blanchard, R.L.Gonzalez, H.D.Kim, S.Chu, and J.D.Puglisi (2005).
Site-specific labeling of the ribosome for single-molecule spectroscopy.
  Nucleic Acids Res, 33, 182-189.  
15840820 M.Guillier, F.Allemand, M.Graffe, S.Raibaud, F.Dardel, M.Springer, and C.Chiaruttini (2005).
The N-terminal extension of Escherichia coli ribosomal protein L20 is important for ribosome assembly, but dispensable for translational feedback control.
  RNA, 11, 728-738.  
16287167 M.J.Suh, D.M.Hamburg, S.T.Gregory, A.E.Dahlberg, and P.A.Limbach (2005).
Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry.
  Proteomics, 5, 4818-4831.  
16244134 M.N.Lambert, J.A.Hoerter, M.J.Pereira, and N.G.Walter (2005).
Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA.
  RNA, 11, 1688-1700.  
16319883 M.W.Talkington, G.Siuzdak, and J.R.Williamson (2005).
An assembly landscape for the 30S ribosomal subunit.
  Nature, 438, 628-632.  
16097941 N.M.Parakhnevitch, A.A.Malygin, and G.G.Karpova (2005).
Recombinant human ribosomal protein S16: expression, purification, refolding, and structural stability.
  Biochemistry (Mosc), 70, 777-781.  
16272105 P.B.Moore (2005).
Structural biology. A ribosomal coup: E. coli at last!
  Science, 310, 793-795.  
15950868 P.B.Moore, and T.A.Steitz (2005).
The ribosome revealed.
  Trends Biochem Sci, 30, 281-283.  
15821981 P.Giavalisco, D.Wilson, T.Kreitler, H.Lehrach, J.Klose, J.Gobom, and P.Fucini (2005).
High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome.
  Plant Mol Biol, 57, 577-591.  
15766539 S.Dutta, and H.M.Berman (2005).
Large macromolecular complexes in the Protein Data Bank: a status report.
  Structure, 13, 381-388.  
16246728 S.Ferreira-Cerca, G.Pöll, P.E.Gleizes, H.Tschochner, and P.Milkereit (2005).
Roles of eukaryotic ribosomal proteins in maturation and transport of pre-18S rRNA and ribosome function.
  Mol Cell, 20, 263-275.  
15811917 S.Ghosh, and S.Joseph (2005).
Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit.
  RNA, 11, 657-667.  
15995195 S.T.Gregory, J.F.Carr, D.Rodriguez-Correa, and A.E.Dahlberg (2005).
Mutational analysis of 16S and 23S rRNA genes of Thermus thermophilus.
  J Bacteriol, 187, 4804-4812.  
15930627 T.Auerbach-Nevo, R.Zarivach, M.Peretz, and A.Yonath (2005).
Reproducible growth of well diffracting ribosomal crystals.
  Acta Crystallogr D Biol Crystallogr, 61, 713-719.  
15604402 A.Chworos, I.Severcan, A.Y.Koyfman, P.Weinkam, E.Oroudjev, H.G.Hansma, and L.Jaeger (2004).
Building programmable jigsaw puzzles with RNA.
  Science, 306, 2068-2072.  
15193314 A.K.Henras, C.Dez, and Y.Henry (2004).
RNA structure and function in C/D and H/ACA s(no)RNPs.
  Curr Opin Struct Biol, 14, 335-343.  
15487937 A.Yonath, and A.Bashan (2004).
Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
  Annu Rev Microbiol, 58, 233-251.  
15062075 C.Abad-Zapatero (2004).
Notes of a protein crystallographer; our unsung heroes.
  Structure, 12, 523-527.  
15096641 C.Herve du Penhoat, H.S.Atreya, Y.Shen, G.Liu, T.B.Acton, R.Xiao, Z.Li, D.Murray, G.T.Montelione, and T.Szyperski (2004).
The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold.
  Protein Sci, 13, 1407-1416.
PDB code: 1qxf
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.
  Cell, 118, 465-475.  
14976550 C.M.Spahn, M.G.Gomez-Lorenzo, R.A.Grassucci, R.Jørgensen, G.R.Andersen, R.Beckmann, P.A.Penczek, J.P.Ballesta, and J.Frank (2004).
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
  EMBO J, 23, 1008-1019.
PDB codes: 1s1h 1s1i
15454463 C.S.Tung, and K.Y.Sanbonmatsu (2004).
Atomic model of the Thermus thermophilus 70S ribosome developed in silico.
  Biophys J, 87, 2714-2722.
PDB codes: 1twt 1twv
15272118 D.H.Mathews (2004).
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.
  RNA, 10, 1178-1190.  
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.