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PDBsum entry 1jgo
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protein dna_rna links
Ribosome PDB id
1jgo
Contents
Protein chains
234 a.a.* *
206 a.a.* *
208 a.a.* *
150 a.a.* *
101 a.a.* *
155 a.a.* *
138 a.a.* *
127 a.a.* *
98 a.a.* *
119 a.a.* *
124 a.a.* *
125 a.a.* *
60 a.a.* *
88 a.a.* *
83 a.a.* *
104 a.a.* *
73 a.a.* *
80 a.a.* *
99 a.a.* *
24 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
1jgo
Name: Ribosome
Title: The path of messenger RNA through the ribosome. This file, 1jgo, contains the 30s ribosome subunit, three tRNA, and mRNA molecules. 50s ribosome subunit is in the file 1giy
Structure: 30s 16s ribosomal RNA. Chain: a. tRNA(phe). Chain: b, c. Engineered: yes. Other_details: a-site tRNA chain b, p-site tRNA chain c. tRNA(phe). Chain: d. Engineered: yes.
Source: Thermus thermophilus. Organism_taxid: 274. Synthetic: yes. Other_details: sequence naturally occurs in saccharomyces cerevisiae. Organism_taxid: 274
Resolution:
5.60Å     R-factor:   not given    
Authors: G.Z.Yusupova,M.M.Yusupov,J.H.D.Cate,H.F.Noller
Key ref:
G.Z.Yusupova et al. (2001). The path of messenger RNA through the ribosome. Cell, 106, 233-241. PubMed id: 11511350 DOI: 10.1016/S0092-8674(01)00435-4
Date:
26-Jun-01     Release date:   20-Jul-01    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		256 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		209 a.a.
208 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		162 a.a.
150 a.a.
Protein chain
Q5SLP8  (RS6_THET8) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
P0DOY9  (RS8_THET8) -  Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		126 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P0DOY6  (RS14Z_THET8) -  Small ribosomal subunit protein uS14 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
P0DOY7  (RS17_THET8) -  Small ribosomal subunit protein uS17 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		105 a.a.
104 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		93 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		106 a.a.
99 a.a.*
Protein chain
Q5SIH3  (RSHX_THET8) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		27 a.a.
24 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

DNA/RNA chains
  U-U-G-U-U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G- ... 1519 bases
  G-C-G-G-A-U-U-U-A-2MG-C-U-C-A-G-H2U-H2U-G-G-G-A-G-A-G-C-M2G-C-C-A-G-A-OMC-U-OM 76 bases
  G-C-G-G-A-U-U-U-A-2MG-C-U-C-A-G-H2U-H2U-G-G-G-A-G-A-G-C-M2G-C-C-A-G-A-OMC-U-OM 76 bases
  U-C-C-G-U-G-A-4SU-A-A-C-A-A-A-G-C-G-G-H2U-H2U-A-U-G-U-A-C-C-G-G-A-U-U-U-U-U-A- 74 bases
  G-G-C-A-A-G-G-A-G-G-U-A-A-A-A-U-U-U-U-U-U-A-A-A-A-A-A 27 bases

 Enzyme reactions 
   Enzyme class: Chains E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/S0092-8674(01)00435-4 Cell 106:233-241 (2001)
PubMed id: 11511350  
 
 
The path of messenger RNA through the ribosome.
G.Z.Yusupova, M.M.Yusupov, J.H.Cate, H.F.Noller.
 
  ABSTRACT  
 
Using X-ray crystallography, we have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 A resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-Dalgarno helix is bound in a large cleft between the head and the back of the platform. At the interface, only about eight nucleotides (-1 to +7), centered on the junction between the A and P codons, are exposed, and bond almost exclusively to 16S rRNA. The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Nucleotide Sequences of the Three Model mRNAs Used in this StudyThe Shine-Dalgarno sequence (S/D), and P- and A-site codons are underlined. The self-complementary sequences forming the putative A-site helix in MF36 mRNA are overlined 		Figure 2.
Figure 2. Fourier Difference Maps of mRNAs(A) 7 Å Fourier difference map of MK27 mRNA with the mRNA model (yellow) docked, showing the position of the Shine-Dalgarno (S/D) helix (magenta) and the positions of the A- and P-site codons (orange and red, respectively), viewed from the top of the 30S ribosomal subunit.(B) Difference map of the MF36 mRNA, showing a four-base-pair tetraloop helix (A-site helix) fitted to the extra density at the A site.(C) Same as for (B), except that the A-tRNA anticodon stem-loop (green) is shown in the position observed experimentally in the A-tRNA difference map (Yusupov et al., 2001), in place of the A-site mRNA helix. The five-nucleotide (GGAGG/CCUCC) core of the Shine-Dalgarno interaction is shown in magenta, and the rest of the 16S rRNA tail in cyan
 
  The above figures are reprinted by permission from Cell Press: Cell (2001, 106, 233-241) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22522823 R.Melero, G.Buchwald, R.Castaño, M.Raabe, D.Gil, M.Lázaro, H.Urlaub, E.Conti, and O.Llorca (2012).
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22664983 S.Melnikov, A.Ben-Shem, N.Garreau de Loubresse, L.Jenner, G.Yusupova, and M.Yusupov (2012).
One core, two shells: bacterial and eukaryotic ribosomes.
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21539788 C.Y.Liu, M.T.Qureshi, and T.H.Lee (2011).
Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
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21399643 D.N.Ermolenko, and H.F.Noller (2011).
mRNA translocation occurs during the second step of ribosomal intersubunit rotation.
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21113134 I.S.Abaeva, A.Marintchev, V.P.Pisareva, C.U.Hellen, and T.V.Pestova (2011).
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21245352 J.Zhu, A.Korostelev, D.A.Costantino, J.P.Donohue, H.F.Noller, and J.S.Kieft (2011).
Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
  Proc Natl Acad Sci U S A, 108, 1839-1844.
PDB codes: 3pyn 3pyo 3pyq 3pyr 3pys 3pyt 3pyu 3pyv
21076851 N.Malys, and J.E.McCarthy (2011).
Translation initiation: variations in the mechanism can be anticipated.
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21623367 T.Becker, J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, H.Sieber, B.A.Motaal, T.Mielke, O.Berninghausen, and R.Beckmann (2011).
Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
  Nat Struct Mol Biol, 18, 715-720.
PDB code: 3izq
21448132 V.P.Pisareva, M.A.Skabkin, C.U.Hellen, T.V.Pestova, and A.V.Pisarev (2011).
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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.
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20034956 A.A.Malygin, and G.G.Karpova (2010).
Structural motifs of the bacterial ribosomal proteins S20, S18 and S16 that contact rRNA present in the eukaryotic ribosomal proteins S25, S26 and S27A, respectively.
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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
20852642 C.L.Ng, K.Lang, N.A.Meenan, A.Sharma, A.C.Kelley, C.Kleanthous, and V.Ramakrishnan (2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
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PDB codes: 2xfz 2xg0 2xg1 2xg2
20235828 J.Frank, and R.L.Gonzalez (2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
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20360683 J.Wen, and S.Brogna (2010).
Splicing-dependent NMD does not require the EJC in Schizosaccharomyces pombe.
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20584896 K.E.Berry, S.Waghray, and J.A.Doudna (2010).
The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit.
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21059903 K.Papenfort, M.Bouvier, F.Mika, C.M.Sharma, and J.Vogel (2010).
Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA.
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20400952 L.B.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
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PDB codes: 3i8f 3i8g 3i8h 3i8i 3i9b 3i9c 3i9d 3i9e
20686685 M.Siwiak, and P.Zielenkiewicz (2010).
A comprehensive, quantitative, and genome-wide model of translation.
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20007152 M.Y.Chou, and K.Y.Chang (2010).
An intermolecular RNA triplex provides insight into structural determinants for the pseudoknot stimulator of -1 ribosomal frameshifting.
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Protein folding and aggregation in bacteria.
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20534490 S.Kurata, K.H.Nielsen, S.F.Mitchell, J.R.Lorsch, A.Kaji, and H.Kaji (2010).
Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP.
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20151411 X.Ge, and B.Roux (2010).
Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
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The human IGF1R IRES likely operates through a Shine-Dalgarno-like interaction with the G961 loop (E-site) of the 18S rRNA and is kinetically modulated by a naturally polymorphic polyU loop.
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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.
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19822758 A.Korostelev, M.Laurberg, and H.F.Noller (2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
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19203580 A.Marintchev, K.A.Edmonds, B.Marintcheva, E.Hendrickson, M.Oberer, C.Suzuki, B.Herdy, N.Sonenberg, and G.Wagner (2009).
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19638248 A.Rich (2009).
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  Q Rev Biophys, 42, 117-137.  
19416977 A.S.Spirin (2009).
The ribosome as a conveying thermal ratchet machine.
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19539793 C.U.Hellen (2009).
IRES-induced conformational changes in the ribosome and the mechanism of translation initiation by internal ribosomal entry.
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18621088 D.P.Giedroc, and P.V.Cornish (2009).
Frameshifting RNA pseudoknots: structure and mechanism.
  Virus Res, 139, 193-208.
PDB codes: 2rp0 2rp1
19129232 E.Babaylova, D.Graifer, A.Malygin, J.Stahl, I.Shatsky, and G.Karpova (2009).
Positioning of subdomain IIId and apical loop of domain II of the hepatitis C IRES on the human 40S ribosome.
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19156357 F.Cava, A.Hidalgo, and J.Berenguer (2009).
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  Extremophiles, 13, 213-231.  
19627501 F.Garza-Sánchez, S.Shoji, K.Fredrick, and C.S.Hayes (2009).
RNase II is important for A-site mRNA cleavage during ribosome pausing.
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19628688 G.Chen, K.Y.Chang, M.Y.Chou, C.Bustamante, and I.Tinoco (2009).
Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting.
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19469554 G.Y.Soung, J.L.Miller, H.Koc, and E.C.Koc (2009).
Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes.
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19930585 H.Yang (2009).
In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure.
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19547922 J.J.Jo, and J.S.Shin (2009).
Construction of intragenic synthetic riboswitches for detection of a small molecule.
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Phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis.
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Footprinting analysis of BWYV pseudoknot-ribosome complexes.
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19812214 M.H.Mazauric, Y.Seol, S.Yoshizawa, K.Visscher, and D.Fourmy (2009).
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Non-canonical RNA arrangement in T4-even phages: accommodated ribosome binding site at the gene 26-25 intercistronic junction.
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Selection and characterization of small molecules that bind the HIV-1 frameshift site RNA.
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19825982 R.Moreno, S.Marzi, P.Romby, and F.Rojo (2009).
The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation.
  Nucleic Acids Res, 37, 7678-7690.  
19779460 S.Chiba, A.Lamsa, and K.Pogliano (2009).
A ribosome-nascent chain sensor of membrane protein biogenesis in Bacillus subtilis.
  EMBO J, 28, 3461-3475.  
19129224 T.Dale, R.P.Fahlman, M.Olejniczak, and O.C.Uhlenbeck (2009).
Specificity of the ribosomal A site for aminoacyl-tRNAs.
  Nucleic Acids Res, 37, 1202-1210.  
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.
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19561193 Y.Yu, A.Marintchev, V.G.Kolupaeva, A.Unbehaun, T.Veryasova, S.C.Lai, P.Hong, G.Wagner, C.U.Hellen, and T.V.Pestova (2009).
Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing.
  Nucleic Acids Res, 37, 5167-5182.  
18369869 A.Görg, C.Lück, and W.Weiss (2008).
Sample prefractionation in granulated sephadex IEF gels.
  Methods Mol Biol, 424, 277-286.  
18758445 A.Simonetti, S.Marzi, A.G.Myasnikov, A.Fabbretti, M.Yusupov, C.O.Gualerzi, and B.P.Klaholz (2008).
Structure of the 30S translation initiation complex.
  Nature, 455, 416-420.  
18464793 A.V.Pisarev, V.G.Kolupaeva, M.M.Yusupov, C.U.Hellen, and T.V.Pestova (2008).
Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes.
  EMBO J, 27, 1609-1621.  
18367719 D.Dulude, G.Théberge-Julien, L.Brakier-Gingras, and N.Heveker (2008).
Selection of peptides interfering with a ribosomal frameshift in the human immunodeficiency virus type 1.
  RNA, 14, 981-991.  
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.  
18310103 G.S.Kopeina, Z.A.Afonina, K.V.Gromova, V.A.Shirokov, V.D.Vasiliev, and A.S.Spirin (2008).
Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA.
  Nucleic Acids Res, 36, 2476-2488.  
18708582 J.Dong, J.S.Nanda, H.Rahman, M.R.Pruitt, B.S.Shin, C.M.Wong, J.R.Lorsch, and A.G.Hinnebusch (2008).
Genetic identification of yeast 18S rRNA residues required for efficient recruitment of initiator tRNA(Met) and AUG selection.
  Genes Dev, 22, 2242-2255.  
18755843 J.E.Brock, S.Pourshahian, J.Giliberti, P.A.Limbach, and G.R.Janssen (2008).
Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG.
  RNA, 14, 2159-2169.  
19111653 J.Richards, and J.G.Belasco (2008).
A new window onto translational repression by bacterial sRNAs.
  Mol Cell, 32, 751-753.  
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.  
18365744 K.N.Bulygin, S.Baouz-Drahy, A.Favre, A.G.Ven'iaminova, D.M.Graíífer, and G.G.Karpova (2008).
[The environment of tRNA 3'-terminus in 80S ribosome A and P sites].
  Bioorg Khim, 34, 96.  
18522973 L.M.Chubiz, and C.V.Rao (2008).
Computational design of orthogonal ribosomes.
  Nucleic Acids Res, 36, 4038-4046.  
19111662 M.Bouvier, C.M.Sharma, F.Mika, K.H.Nierhaus, and J.Vogel (2008).
Small RNA binding to 5' mRNA coding region inhibits translational initiation.
  Mol Cell, 32, 827-837.  
18497739 M.Y.Pavlov, A.Antoun, M.Lovmar, and M.Ehrenberg (2008).
Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting.
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18772887 N.M.Wills, M.O'Connor, C.C.Nelson, C.C.Rettberg, W.M.Huang, R.F.Gesteland, and J.F.Atkins (2008).
Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA.
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The ribosome structure controls and directs mRNA entry, translocation and exit dynamics.
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18400176 P.Chandramouli, M.Topf, J.F.Ménétret, N.Eswar, J.J.Cannone, R.R.Gutell, A.Sali, and C.W.Akey (2008).
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PDB codes: 2zkq 2zkr
18367782 S.Cao, and S.J.Chen (2008).
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18953726 S.Marzi, P.Fechter, C.Chevalier, P.Romby, and T.Geissmann (2008).
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18299414 Y.H.Min, A.R.Kwon, E.J.Yoon, M.J.Shim, and E.C.Choi (2008).
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17085569 J.E.Brock, R.L.Paz, P.Cottle, and G.R.Janssen (2007).
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17434125 L.A.Passmore, T.M.Schmeing, D.Maag, D.J.Applefield, M.G.Acker, M.A.Algire, J.R.Lorsch, and V.Ramakrishnan (2007).
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PDB codes: 3bbn 3bbo
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17937620 N.Fischer, A.Paleskava, K.B.Gromadski, A.L.Konevega, M.C.Wahl, H.Stark, and M.V.Rodnina (2007).
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PDB codes: 2dyj 2r1c 2r1g
17868691 R.J.Marcheschi, D.W.Staple, and S.E.Butcher (2007).
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PDB code: 2jtp
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PDB code: 2vaz
17377584 S.Uemura, M.Dorywalska, T.H.Lee, H.D.Kim, J.D.Puglisi, and S.Chu (2007).
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16510876 A.V.Pisarev, V.G.Kolupaeva, V.P.Pisareva, W.C.Merrick, C.U.Hellen, and T.V.Pestova (2006).
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16452425 A.Wietzorrek, H.Schwarz, C.Herrmann, and V.Braun (2006).
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PDB codes: 1vs5 1vs6 1vs7 1vs8
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16680139 F.J.Isaacs, D.J.Dwyer, and J.J.Collins (2006).
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17051149 G.Yusupova, L.Jenner, B.Rees, D.Moras, and M.Yusupov (2006).
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PDB codes: 2hgi 2hgj 2hgp 2hgq 2hgr 2hgu
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PDB codes: 2j00 2j01 2j02 2j03
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17000902 P.V.Cornish, S.N.Stammler, and D.P.Giedroc (2006).
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PDB codes: 2ap0 2ap5
16730356 S.E.Walker, and K.Fredrick (2006).
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16595798 S.Nonin-Lecomte, B.Felden, and F.Dardel (2006).
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PDB code: 2g1w
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16364749 T.W.Dreher, and W.A.Miller (2006).
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15749702 A.A.Komar, and M.Hatzoglou (2005).
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16269538 A.Yassin, K.Fredrick, and A.S.Mankin (2005).
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15755955 B.S.Laursen, H.P.Sørensen, K.K.Mortensen, and H.U.Sperling-Petersen (2005).
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PDB codes: 2avy 2aw4 2aw7 2awb
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PDB code: 2agn
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16257826 D.N.Wilson, and K.H.Nierhaus (2005).
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15811920 I.K.Wower, C.Zwieb, and J.Wower (2005).
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15978079 J.S.Sharp, and D.H.Bechhofer (2005).
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16204455 K.Asano, D.Kurita, K.Takada, T.Konno, A.Muto, and H.Himeno (2005).
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PDB codes: 1yl3 1yl4
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16004388 N.A.Demeshkina, V.A.Stiazhkina, K.N.Bulygin, M.N.Repkova, A.G.Ven'iaminova, and G.G.Karpova (2005).
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16177132 N.M.Abdi, and K.Fredrick (2005).
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16408021 O.Rackham, and J.W.Chin (2005).
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PDB code: 2a43
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PDB codes: 1yg3 1yg4
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15665870 S.Yoshizawa, L.Rasubala, T.Ose, D.Kohda, D.Fourmy, and K.Maenaka (2005).
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PDB code: 1wsu
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PDB codes: 1voq 1vor 1vos 1vou 1vov 1vow 1vox 1voy 1voz 1vp0
15016910 B.Schneider, Z.Morávek, and H.M.Berman (2004).
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15315759 C.M.Spahn, E.Jan, A.Mulder, R.A.Grassucci, P.Sarnow, and J.Frank (2004).
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15146079 H.J.Merianos, J.Wang, and P.B.Moore (2004).
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PDB code: 1s03
14730351 K.L.Holmes, and G.M.Culver (2004).
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15100436 M.J.Trimble, A.Minnicus, and K.P.Williams (2004).
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PDB codes: 1t1m 1t1o
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15060025 U.Mäder, S.Hennig, M.Hecker, and G.Homuth (2004).
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  RNA, 9, 982-992.  
14627813 A.Tabb-Massey, J.M.Caffrey, P.Logsden, S.Taylor, J.O.Trent, and S.R.Ellis (2003).
Ribosomal proteins Rps0 and Rps21 of Saccharomyces cerevisiae have overlapping functions in the maturation of the 3' end of 18S rRNA.
  Nucleic Acids Res, 31, 6798-6805.  
12511961 B.P.Klaholz, T.Pape, A.V.Zavialov, A.G.Myasnikov, E.V.Orlova, B.Vestergaard, M.Ehrenberg, and M.van Heel (2003).
Structure of the Escherichia coli ribosomal termination complex with release factor 2.
  Nature, 421, 90-94.
PDB code: 1ml5
12649494 E.H.Williams, and T.D.Fox (2003).
Antagonistic signals within the COX2 mRNA coding sequence control its translation in Saccharomyces cerevisiae mitochondria.
  RNA, 9, 419-431.  
12554858 E.P.Plant, K.L.Jacobs, J.W.Harger, A.Meskauskas, J.L.Jacobs, J.L.Baxter, A.N.Petrov, and J.D.Dinman (2003).
The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting.
  RNA, 9, 168-174.  
12937172 F.Robert, and L.Brakier-Gingras (2003).
A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome.
  J Biol Chem, 278, 44913-44920.  
12548626 G.M.Culver (2003).
Assembly of the 30S ribosomal subunit.
  Biopolymers, 68, 234-249.  
12809609 H.Gao, J.Sengupta, M.Valle, A.Korostelev, N.Eswar, S.M.Stagg, P.Van Roey, R.K.Agrawal, S.C.Harvey, A.Sali, M.S.Chapman, and J.Frank (2003).
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
  Cell, 113, 789-801.
PDB codes: 1p6g 1p85 1p86 1p87
12949089 J.S.Sharp, and D.H.Bechhofer (2003).
Effect of translational signals on mRNA decay in Bacillus subtilis.
  J Bacteriol, 185, 5372-5379.  
14532006 M.R.Sharma, E.C.Koc, P.P.Datta, T.M.Booth, L.L.Spremulli, and R.K.Agrawal (2003).
Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins.
  Cell, 115, 97.  
12677067 M.Valle, R.Gillet, S.Kaur, A.Henne, V.Ramakrishnan, and J.Frank (2003).
Visualizing tmRNA entry into a stalled ribosome.
  Science, 300, 127-130.
PDB code: 1zc8
12970189 P.Licznar, N.Mejlhede, M.F.Prère, N.Wills, R.F.Gesteland, J.F.Atkins, and O.Fayet (2003).
Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs.
  EMBO J, 22, 4770-4778.  
12615010 P.Romby, and M.Springer (2003).
Bacterial translational control at atomic resolution.
  Trends Genet, 19, 155-161.  
12554856 S.Joseph (2003).
After the ribosome structure: how does translocation work?
  RNA, 9, 160-164.  
12717454 T.M.Hansen, P.V.Baranov, I.P.Ivanov, R.F.Gesteland, and J.F.Atkins (2003).
Maintenance of the correct open reading frame by the ribosome.
  EMBO Rep, 4, 499-504.  
12511960 U.B.Rawat, A.V.Zavialov, J.Sengupta, M.Valle, R.A.Grassucci, J.Linde, B.Vestergaard, M.Ehrenberg, and J.Frank (2003).
A cryo-electron microscopic study of ribosome-bound termination factor RF2.
  Nature, 421, 87-90.
PDB codes: 1mi6 1mvr
11871658 C.Bertrand, M.F.Prère, R.F.Gesteland, J.F.Atkins, and O.Fayet (2002).
Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression.
  RNA, 8, 16-28.  
12244297 C.S.Tung, S.Joseph, and K.Y.Sanbonmatsu (2002).
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
  Nat Struct Biol, 9, 750-755.
PDB code: 1m5g
11959559 D.E.Low, J.de Azavedo, K.Weiss, T.Mazzulli, M.Kuhn, D.Church, K.Forward, G.Zhanel, A.Simor, and A.McGeer (2002).
Antimicrobial resistance among clinical isolates of Streptococcus pneumoniae in Canada during 2000.
  Antimicrob Agents Chemother, 46, 1295-1301.  
12166646 G.A.Otto, P.J.Lukavsky, A.M.Lancaster, P.Sarnow, and J.D.Puglisi (2002).
Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction.
  RNA, 8, 913-923.  
12138121 G.Hirokawa, M.C.Kiel, A.Muto, G.Kawai, K.Igarashi, H.Kaji, and A.Kaji (2002).
Binding of ribosome recycling factor to ribosomes, comparison with tRNA.
  J Biol Chem, 277, 35847-35852.  
11980724 G.Hirokawa, M.C.Kiel, A.Muto, M.Selmer, V.S.Raj, A.Liljas, K.Igarashi, H.Kaji, and A.Kaji (2002).
Post-termination complex disassembly by ribosome recycling factor, a functional tRNA mimic.
  EMBO J, 21, 2272-2281.  
11943544 G.Stahl, G.P.McCarty, and P.J.Farabaugh (2002).
Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding.
  Trends Biochem Sci, 27, 178-183.  
12149516 J.K.Barry, and W.A.Miller (2002).
A -1 ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA.
  Proc Natl Acad Sci U S A, 99, 11133-11138.  
12270832 J.Ma, A.Campbell, and S.Karlin (2002).
Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures.
  J Bacteriol, 184, 5733-5745.  
12217519 J.W.Harger, A.Meskauskas, and J.D.Dinman (2002).
An "integrated model" of programmed ribosomal frameshifting.
  Trends Biochem Sci, 27, 448-454.  
12049747 K.Fredrick, and H.F.Noller (2002).
Accurate translocation of mRNA by the ribosome requires a peptidyl group or its analog on the tRNA moving into the 30S P site.
  Mol Cell, 9, 1125-1131.  
12372306 L.Lancaster, M.C.Kiel, A.Kaji, and H.F.Noller (2002).
Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing.
  Cell, 111, 129-140.  
11867615 M.A.Schäfer, A.O.Tastan, S.Patzke, G.Blaha, C.M.Spahn, D.N.Wilson, and K.H.Nierhaus (2002).
Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit.
  J Biol Chem, 277, 19095-19105.  
12145214 M.Selmer, and X.D.Su (2002).
Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.
  EMBO J, 21, 4145-4153.
PDB code: 1lva
12093756 M.Valle, J.Sengupta, N.K.Swami, R.A.Grassucci, N.Burkhardt, K.H.Nierhaus, R.K.Agrawal, and J.Frank (2002).
Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.
  EMBO J, 21, 3557-3567.
PDB codes: 1ls2 1lu3
11897659 P.V.Baranov, R.F.Gesteland, and J.F.Atkins (2002).
Release factor 2 frameshifting sites in different bacteria.
  EMBO Rep, 3, 373-377.  
12144927 S.Cheley, L.Q.Gu, and H.Bayley (2002).
Stochastic sensing of nanomolar inositol 1,4,5-trisphosphate with an engineered pore.
  Chem Biol, 9, 829-838.  
11967318 S.P.Fletcher, and R.J.Jackson (2002).
Pestivirus internal ribosome entry site (IRES) structure and function: elements in the 5' untranslated region important for IRES function.
  J Virol, 76, 5024-5033.  
11909526 V.Ramakrishnan (2002).
Ribosome structure and the mechanism of translation.
  Cell, 108, 557-572.  
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.  
11566123 G.M.Culver (2001).
Meanderings of the mRNA through the ribosome.
  Structure, 9, 751-758.  
12762026 G.Stahl, S.Ben Salem, Z.Li, G.McCarty, A.Raman, M.Shah, and P.J.Farabaugh (2001).
Programmed +1 translational frameshifting in the yeast Saccharomyces cerevisiae results from disruption of translational error correction.
  Cold Spring Harb Symp Quant Biol, 66, 249-258.  
12762008 H.F.Noller, M.M.Yusupov, G.Z.Yusupova, A.Baucom, K.Lieberman, L.Lancaster, A.Dallas, K.Fredrick, T.N.Earnest, and J.H.Cate (2001).
Structure of the ribosome at 5.5 A resolution and its interactions with functional ligands.
  Cold Spring Harb Symp Quant Biol, 66, 57-66.  
12762025 I.Brierley, and S.Pennell (2001).
Structure and function of the stimulatory RNAs involved in programmed eukaryotic-1 ribosomal frameshifting.
  Cold Spring Harb Symp Quant Biol, 66, 233-248.  
11743004 J.B.Mansell, D.Guévremont, E.S.Poole, and W.P.Tate (2001).
A dynamic competition between release factor 2 and the tRNA(Sec) decoding UGA at the recoding site of Escherichia coli formate dehydrogenase H.
  EMBO J, 20, 7284-7293.  
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.

 

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