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PDBsum entry 1c59

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Ribosome PDB id
1c59
Jmol
Contents
Ligands
__N-__N-__N-__N-
__N-__N-__N-__N-
__N-__N-__N
×12
__N-__N-__N-__N-
__N-__N-__N-__N-
__N-__N
×4
__N-__N-__N-__N-
__N-__N-__N-__N-
__N-__N-__N-__N
×4
__N-__N-__N-__N-
__N-__N-__N-__N
×2
__N ×3
__N-__N-__N-__N-
__N-__N-__N
×2
__N-__N-__N-__N-
__N
×20
__N-__N-__N-__N-
__N-__N-__N-__N-
__N
Superseded by: 1dv4
PDB id:
1c59
Name: Ribosome
Title: Partial structure of 16s RNA of the small ribosomal subunit from thermus thermophilus
Structure: 16s ribosomal RNA. Chain: a
Source: Thermus thermophilus
Resolution:
4.50Å     R-factor:   not given    
Authors: A.Tocilj,F.Schlunzen,D.Janell,M.Gluhmann,H.Hansen,J.Harms, A.Bashan,H.Bartels,I.Agmon,F.Franceschi,A.Yonath
Key ref:
A.Tocilj et al. (1999). The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site. Proc Natl Acad Sci U S A, 96, 14252-14257. PubMed id: 10588692 DOI: 10.1073/pnas.96.25.14252
Date:
28-Oct-99     Release date:   02-Dec-99    
 Headers
 References

 

 
DOI no: 10.1073/pnas.96.25.14252 Proc Natl Acad Sci U S A 96:14252-14257 (1999)
PubMed id: 10588692  
 
 
The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site.
A.Tocilj, F.Schlünzen, D.Janell, M.Glühmann, H.A.Hansen, J.Harms, A.Bashan, H.Bartels, I.Agmon, F.Franceschi, A.Yonath.
 
  ABSTRACT  
 
The electron density map of the small ribosomal subunit from Thermus thermophilus, constructed at 4.5 A resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal RNA and proteins. Unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein S13 at a position compatible with previous assignments, whereas the surface of S11 was localized at a distance of about twice its diameter from the site suggested for its center by neutron scattering. Proteins S5 and S7, whose structures have been determined crystallographically, were visually placed in the map with no alterations in their conformations. Regions suitable to host the fold of protein S15 were detected in several positions, all at a significant distance from the location of this protein in the neutron scattering map. Targeting the 16S RNA region, where mRNA docks to allow the formation of the initiation complex by a mercurated mRNA analog, led to the characterization of its vicinity.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Parts of the T30S electron density maps at different stages of structure determination from 6 to 4.5 Å (contour level 1 SD, unless otherwise mentioned). (a) A helix-bulge-helix region, traced at 6 Å resolution. (b and c) Views of A-form RNA regions within the 4.5 Å map. (d) Part of the 4.5 Å map, contoured at 1.5 (cyan) and 2.5 (green-yellow) SD. These levels were chosen to avoid background noise and to highlight the phosphates in the RNA backbone, respectively. (e and f) The regions of the 4.5 Å map assigned to protein TS5 and TS15, respectively. In f, the less well defined helix was found to be flexible in isolation by NMR and x-ray (21).
Figure 4.
Fig. 4. The regions that became interpretable by the incorporation of the anomalous data, shown as white objects. The insert focuses on one of them, traced later as helix-bulge-helix motif.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
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Enabling technologies in discovery: the 2009 Nobel Prize and its implications in antibiotic design.
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19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
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17565764 O.Schiemann, and T.F.Prisner (2007).
Long-range distance determinations in biomacromolecules by EPR spectroscopy.
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15930627 T.Auerbach-Nevo, R.Zarivach, M.Peretz, and A.Yonath (2005).
Reproducible growth of well diffracting ribosomal crystals.
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RNA conformational classes.
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12925991 A.Bashan, R.Zarivach, F.Schluenzen, I.Agmon, J.Harms, T.Auerbach, D.Baram, R.Berisio, H.Bartels, H.A.Hansen, P.Fucini, D.Wilson, M.Peretz, M.Kessler, and A.Yonath (2003).
Ribosomal crystallography: peptide bond formation and its inhibition.
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14573953 G.Rudenko, L.Henry, C.Vonrhein, G.Bricogne, and J.Deisenhofer (2003).
'MAD'ly phasing the extracellular domain of the LDL receptor: a medium-sized protein, large tungsten clusters and multiple non-isomorphous crystals.
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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.
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12490711 J.M.Zimmerman, and L.J.Maher (2002).
In vivo selection of spectinomycin-binding RNAs.
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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.
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11812838 A.V.Kubarenko, P.V.Sergiev, A.A.Bogdanov, R.Brimacombe, and O.A.Dontsova (2001).
A protonated base pair participating in rRNA tertiary structural interactions.
  Nucleic Acids Res, 29, 5067-5070.  
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.  
12762005 D.E.Brodersen, A.P.Carter, W.M.Clemons, R.J.Morgan-Warren, F.V.Murphy, J.M.Ogle, M.J.Tarry, B.T.Wimberly, and V.Ramakrishnan (2001).
Atomic structures of the 30S subunit and its complexes with ligands and antibiotics.
  Cold Spring Harb Symp Quant Biol, 66, 17-32.  
11214183 D.I.Juzumiene, and P.Wollenzien (2001).
Arrangement of the central pseudoknot region of 16S rRNA in the 30S ribosomal subunit determined by site-directed 4-thiouridine crosslinking.
  RNA, 7, 71-84.  
11828423 D.M.Lilley (2001).
The ribosome functions as a ribozyme.
  Chembiochem, 2, 31-35.  
11593008 J.Sengupta, R.K.Agrawal, and J.Frank (2001).
Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA.
  Proc Natl Acad Sci U S A, 98, 11991-11996.  
11296217 M.Pioletti, F.Schlünzen, J.Harms, R.Zarivach, M.Glühmann, H.Avila, A.Bashan, H.Bartels, T.Auerbach, C.Jacobi, T.Hartsch, A.Yonath, and F.Franceschi (2001).
Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3.
  EMBO J, 20, 1829-1839.
PDB codes: 1i94 1i95 1i96 1i97
11258942 P.B.Moore (2001).
The ribosome at atomic resolution.
  Biochemistry, 40, 3243-3250.  
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.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
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.  
10871387 E.Cayama, A.Yépez, F.Rotondo, E.Bandeira, A.C.Ferreras, and F.J.Triana-Alonso (2000).
New chromatographic and biochemical strategies for quick preparative isolation of tRNA.
  Nucleic Acids Res, 28, E64.  
11105763 F.Robert, M.Gagnon, D.Sans, S.Michnick, and L.Brakier-Gingras (2000).
Mapping of the RNA recognition site of Escherichia coli ribosomal protein S7.
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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.  
11000271 J.W.Noah, T.Shapkina, and P.Wollenzien (2000).
UV-induced crosslinks in the 16S rRNAs of Escherichia coli, Bacillus subtilis and Thermus aquaticus and their implications for ribosome structure and photochemistry.
  Nucleic Acids Res, 28, 3785-3792.  
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.  
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
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.  
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
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.  
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.  
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.  
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.