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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
1pnx
Jmol
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. *
DNA/RNA
* Residue conservation analysis
PDB id:
1pnx
Name: Ribosome
Title: Crystal structure of the wild type ribosome from e. Coli, 30s subunit of 70s ribosome. This file, 1pnx, contains only molecules of the 30s ribosomal subunit. The 50s subunit is in the PDB file 1pny.
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: Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
Biol. unit: 20mer (from PQS)
Resolution:
9.50Å     R-factor:   0.389     R-free:   0.407
Authors: A.Vila-Sanjurjo,W.K.Ridgeway,V.Seymaner,W.Zhang,S.Santoso, K.Yu,J.H.D.Cate
Key ref:
A.Vila-Sanjurjo et al. (2003). X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli. Proc Natl Acad Sci U S A, 100, 8682-8687. PubMed id: 12853578 DOI: 10.1073/pnas.1133380100
Date:
13-Jun-03     Release date:   15-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

 

 
DOI no: 10.1073/pnas.1133380100 Proc Natl Acad Sci U S A 100:8682-8687 (2003)
PubMed id: 12853578  
 
 
X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli.
A.Vila-Sanjurjo, W.K.Ridgeway, V.Seymaner, W.Zhang, S.Santoso, K.Yu, J.H.Cate.
 
  ABSTRACT  
 
Protein biosynthesis on the ribosome requires accurate reading of the genetic code in mRNA. Two conformational rearrangements in the small ribosomal subunit, a closing of the head and body around the incoming tRNA and an RNA helical switch near the mRNA decoding site, have been proposed to select for complementary base-pairing between mRNA codons and tRNA anticodons. We determined x-ray crystal structures of the WT and a hyper-accurate variant of the Escherichia coli ribosome at resolutions of 10 and 9 A, respectively, revealing that formation of the intact 70S ribosome from its two subunits closes the conformation of the head of the small subunit independent of mRNA decoding. Moreover, no change in the conformation of the switch helix is observed in two steps of tRNA discrimination. These 70S ribosome structures indicate that mRNA decoding is coupled primarily to movement of the small subunit body, consistent with previous proposals, whereas closing of the head and the helical switch may function in other steps of protein synthesis.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Superpositions of ribosomal subunit structures. (a) Position of the L1 stalk in the smD E. coli ribosome structure (blue) compared with that in the T. thermophilus 70S ribosome (red). The 50S subunit is shown from the 30S interface side. The arrow indicates the direction of motion required to move from the closed to open position of the L1 stalk. (b) Stereoview comparing the open 30S subunit conformation to the small subunit in the E. coli smD ribosome. Difference vectors between all conserved phosphorus atoms in the small subunit are shown. Arrows indicate the direction of movement in going from the open conformation to that in the intact ribosome. The large subunit (gray), mRNA (blue), A-site tRNA (light green), and P-site tRNA (light blue) bound to the E. coli smD ribosome are shown for reference. Other components of the ribosome are marked as in Fig. 1. (c) Comparison of the open 30S subunit conformation to the small subunit in the T. thermophilus 70S ribosome structure. Difference vectors are shown as described above. The orientation is the same as in b.(d) Stereoview comparing the closed 30S subunit conformation to the small subunit in the E. coli smD ribosome. (e) Comparison of the closed 30S subunit conformation to the small subunit in the T. thermophilus 70S ribosome structure. The orientation is the same as in d. 		Figure 3.
Fig. 3. Conformation of the 70S ribosome in the switch helix region. (a) Difference electron density map comparing WT and smD 70S ribosomes from E. coli. The difference map was calculated by using observed diffraction amplitudes from both crystal forms, as described in Materials and Methods. The smD ribosomes contain mRNA, P-site tRNA^fMet (P-tRNA, Upper Right) and noncognate A-site tRNA^fMet at 50% occupancy (A-tRNA, Lower Right). (Left) A top view of the ribosome is shown with the A site, P site, and E site indicated to the left of the small subunit. The tRNAs are viewed from the perspective of the E site, as indicated by the arrow. The color scheme of the ribosome complex is the same as in Fig. 1. (b) The same difference electron density map in the switch helix region. (c) Difference electron density map comparing the smD 70S ribosome complex to a model lacking ligands throughout refinement. The positive electron density corresponds to P-site tRNA and mRNA bound to the ribosome. The perspective is the same as in a. (d) The same difference electron density map in the switch helix region. (e) Difference electron density map comparing the smD 70S ribosome complex to a ribosome model that contained streptomycin throughout refinement. The streptomycin binding pocket (sm) is shown. Positive electron density (blue, left) appeared after refinements of the model both in the absence and presence of the antibiotic, whereas negative density appeared only when streptomycin was included in the model. In all panels, difference electron density is contoured at 3.0 and -3.0 SDs from the mean (blue and red, respectively).
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21253384 D.Kurita, A.Muto, and H.Himeno (2011).
tRNA/mRNA Mimicry by tmRNA and SmpB in Trans-Translation.
  J Nucleic Acids, 2011, 130581.  
21383139 J.Fu, J.B.Munro, S.C.Blanchard, and J.Frank (2011).
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
  Proc Natl Acad Sci U S A, 108, 4817-4821.  
20603079 H.S.Zaher, and R.Green (2010).
Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection.
  Mol Cell, 39, 110-120.  
20940705 J.Fu, Y.Hashem, I.Wower, J.Lei, H.Y.Liao, C.Zwieb, J.Wower, and J.Frank (2010).
Visualizing the transfer-messenger RNA as the ribosome resumes translation.
  EMBO J, 29, 3819-3825.
PDB code: 3iz4
19952067 K.Réblová, F.Rázga, W.Li, H.Gao, J.Frank, and J.Sponer (2010).
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
  Nucleic Acids Res, 38, 1325-1340.  
19596816 A.D.Kauffmann, R.J.Campagna, C.B.Bartels, and J.L.Childs-Disney (2009).
Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides.
  Nucleic Acids Res, 37, e121.  
18479505 D.J.Whitehead, C.O.Wilke, D.Vernazobres, and E.Bornberg-Bauer (2008).
The look-ahead effect of phenotypic mutations.
  Biol Direct, 3, 18.  
18713011 R.Stapulionis, Y.Wang, G.T.Dempsey, R.Khudaravalli, K.M.Nielsen, B.S.Cooperman, Y.E.Goldman, and C.R.Knudsen (2008).
Fast in vitro translation system immobilized on a surface via specific biotinylation of the ribosome.
  Biol Chem, 389, 1239-1249.  
17244535 A.Fabbretti, C.L.Pon, S.P.Hennelly, W.E.Hill, J.S.Lodmell, and C.O.Gualerzi (2007).
The real-time path of translation factor IF3 onto and off the ribosome.
  Mol Cell, 25, 285-296.  
17683199 A.L.Manuell, J.Quispe, and S.P.Mayfield (2007).
Structure of the chloroplast ribosome: novel domains for translation regulation.
  PLoS Biol, 5, e209.  
17959652 D.Kurita, R.Sasaki, A.Muto, and H.Himeno (2007).
Interaction of SmpB with ribosome from directed hydroxyl radical probing.
  Nucleic Acids Res, 35, 7248-7255.  
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
17317624 J.B.Munro, R.B.Altman, N.O'Connor, and S.C.Blanchard (2007).
Identification of two distinct hybrid state intermediates on the ribosome.
  Mol Cell, 25, 505-517.  
17157507 M.V.Rodnina, M.Beringer, and W.Wintermeyer (2007).
How ribosomes make peptide bonds.
  Trends Biochem Sci, 32, 20-26.  
16855310 B.DeLaBarre, and A.T.Brunger (2006).
Considerations for the refinement of low-resolution crystal structures.
  Acta Crystallogr D Biol Crystallogr, 62, 923-932.  
16998486 B.S.Schuwirth, J.M.Day, C.W.Hau, G.R.Janssen, A.E.Dahlberg, J.H.Cate, and A.Vila-Sanjurjo (2006).
Structural analysis of kasugamycin inhibition of translation.
  Nat Struct Mol Biol, 13, 879-886.
PDB codes: 1vs5 1vs6 1vs7 1vs8
16380421 L.Brandi, A.Fabbretti, A.La Teana, M.Abbondi, D.Losi, S.Donadio, and C.O.Gualerzi (2006).
Specific, efficient, and selective inhibition of prokaryotic translation initiation by a novel peptide antibiotic.
  Proc Natl Acad Sci U S A, 103, 39-44.  
16699167 L.Brandi, A.Fabbretti, M.Di Stefano, A.Lazzarini, M.Abbondi, and C.O.Gualerzi (2006).
Characterization of GE82832, a peptide inhibitor of translocation interacting with bacterial 30S ribosomal subunits.
  RNA, 12, 1262-1270.  
17000775 R.Rakauskaite, and J.D.Dinman (2006).
An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome.
  Mol Cell Biol, 26, 8992-9002.  
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.  
16314459 C.L.Shenvi, K.C.Dong, E.M.Friedman, J.A.Hanson, and J.H.Cate (2005).
Accessibility of 18S rRNA in human 40S subunits and 80S ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics.
  RNA, 11, 1898-1908.  
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.  
  18074004 J.D.Dinman (2005).
5S rRNA: Structure and Function from Head to Toe.
  Int J Biomed Sci, 1, 2-7.  
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.  
16249344 K.Y.Sanbonmatsu, S.Joseph, and C.S.Tung (2005).
Simulating movement of tRNA into the ribosome during decoding.
  Proc Natl Acad Sci U S A, 102, 15854-15859.  
15989950 M.Diaconu, U.Kothe, F.Schlünzen, N.Fischer, J.M.Harms, A.G.Tonevitsky, H.Stark, M.V.Rodnina, and M.C.Wahl (2005).
Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
  Cell, 121, 991.
PDB codes: 1zav 1zaw 1zax 1zb4
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.  
15972795 N.Ivanova, M.Y.Pavlov, E.Bouakaz, M.Ehrenberg, and L.H.Schiavone (2005).
Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA.
  Nucleic Acids Res, 33, 3529-3539.  
16114868 P.S.Pallan, W.S.Marshall, J.Harp, F.C.Jewett, Z.Wawrzak, B.A.Brown, A.Rich, and M.Egli (2005).
Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal frameshifting motif.
  Biochemistry, 44, 11315-11322.
PDB code: 2a43
15699355 T.R.Sundermeier, D.P.Dulebohn, H.J.Cho, and A.W.Karzai (2005).
A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation.
  Proc Natl Acad Sci U S A, 102, 2316-2321.  
15502846 A.Vila-Sanjurjo, B.S.Schuwirth, C.W.Hau, and J.H.Cate (2004).
Structural basis for the control of translation initiation during stress.
  Nat Struct Mol Biol, 11, 1054-1059.
PDB codes: 1voq 1vor 1vos 1vou 1vov 1vow 1vox 1voy 1voz 1vp0
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
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.  
15166137 E.H.Williams, X.Perez-Martinez, and T.D.Fox (2004).
MrpL36p, a highly diverged L31 ribosomal protein homolog with additional functional domains in Saccharomyces cerevisiae mitochondria.
  Genetics, 167, 65-75.  
15004548 K.B.Gromadski, and M.V.Rodnina (2004).
Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome.
  Nat Struct Mol Biol, 11, 316-322.  
14759365 K.B.Gromadski, and M.V.Rodnina (2004).
Kinetic determinants of high-fidelity tRNA discrimination on the ribosome.
  Mol Cell, 13, 191-200.  
15009191 N.Chumpolkulwong, C.Hori-Takemoto, T.Hosaka, T.Inaoka, T.Kigawa, M.Shirouzu, K.Ochi, and S.Yokoyama (2004).
Effects of Escherichia coli ribosomal protein S12 mutations on cell-free protein synthesis.
  Eur J Biochem, 271, 1127-1134.  
14715921 P.F.Agris (2004).
Decoding the genome: a modified view.
  Nucleic Acids Res, 32, 223-238.  
14659007 J.Frank (2003).
Toward an understanding of the structural basis of translation.
  Genome Biol, 4, 237.  
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 code is shown on the right.