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PDBsum entry 487d

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protein ligands links
Ribosome PDB id
487d
Jmol
Contents
Protein chains
224 a.a. *
135 a.a. *
164 a.a. *
149 a.a. *
133 a.a. *
122 a.a. *
94 a.a. *
Ligands
NH2
FMT
* Residue conservation analysis
PDB id:
487d
Name: Ribosome
Title: Seven ribosomal proteins fitted to a cryo-electron microscopic map of the large 50s subunit at 7.5 angstroms resolution
Structure: Protein (50s l1 ribosomal protein). Chain: h. Protein (50s l2 ribosomal protein). Chain: i. Protein (50s l6 ribosomal protein). Chain: j. Protein (50s l9 ribosomal protein). Chain: k. Protein (50s l11 ribosomal protein).
Source: Thermus thermophilus. Organism_taxid: 274. Geobacillus stearothermophilus. Organism_taxid: 1422. Thermotoga maritima. Organism_taxid: 2336. Escherichia coli. Organism_taxid: 562
Authors: R.Brimacombe,F.Mueller
Key ref:
F.Mueller et al. (2000). The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution. J Mol Biol, 298, 35-59. PubMed id: 10756104 DOI: 10.1006/jmbi.2000.3635
Date:
23-Feb-00     Release date:   10-Apr-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P27150  (RL1_THETH) -  50S ribosomal protein L1
Seq:
Struc:
229 a.a.
224 a.a.*
Protein chain
Pfam   ArchSchema ?
P04257  (RL2_GEOSE) -  50S ribosomal protein L2
Seq:
Struc:
276 a.a.
135 a.a.
Protein chain
Pfam   ArchSchema ?
P02391  (RL6_GEOSE) -  50S ribosomal protein L6
Seq:
Struc:
178 a.a.
164 a.a.
Protein chain
Pfam   ArchSchema ?
P02417  (RL9_GEOSE) -  50S ribosomal protein L9
Seq:
Struc:
149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P29395  (RL11_THEMA) -  50S ribosomal protein L11
Seq:
Struc:
141 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P04450  (RL14_GEOSE) -  50S ribosomal protein L14
Seq:
Struc:
122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25
Seq:
Struc:
94 a.a.
94 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     regulation of translation   2 terms 
  Biochemical function     structural constituent of ribosome     7 terms  

 

 
DOI no: 10.1006/jmbi.2000.3635 J Mol Biol 298:35-59 (2000)
PubMed id: 10756104  
 
 
The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution.
F.Mueller, I.Sommer, P.Baranov, R.Matadeen, M.Stoldt, J.Wöhnert, M.Görlach, M.van Heel, R.Brimacombe.
 
  ABSTRACT  
 
The Escherichia coli 23 S and 5 S rRNA molecules have been fitted helix by helix to a cryo-electron microscopic (EM) reconstruction of the 50 S ribosomal subunit, using an unfiltered version of the recently published 50 S reconstruction at 7.5 A resolution. At this resolution, the EM density shows a well-defined network of fine structural elements, in which the major and minor grooves of the rRNA helices can be discerned at many locations. The 3D folding of the rRNA molecules within this EM density is constrained by their well-established secondary structures, and further constraints are provided by intra and inter-rRNA crosslinking data, as well as by tertiary interactions and pseudoknots. RNA-protein cross-link and foot-print sites on the 23 S and 5 S rRNA were used to position the rRNA elements concerned in relation to the known arrangement of the ribosomal proteins as determined by immuno-electron microscopy. The published X-ray or NMR structures of seven 50 S ribosomal proteins or RNA-protein complexes were incorporated into the EM density. The 3D locations of cross-link and foot-print sites to the 23 S rRNA from tRNA bound to the ribosomal A, P or E sites were correlated with the positions of the tRNA molecules directly observed in earlier reconstructions of the 70 S ribosome at 13 A or 20 A. Similarly, the positions of cross-link sites within the peptidyl transferase ring of the 23 S rRNA from the aminoacyl residue of tRNA were correlated with the locations of the CCA ends of the A and P site tRNA. Sites on the 23 S rRNA that are cross-linked to the N termini of peptides of different lengths were all found to lie within or close to the internal tunnel connecting the peptidyl transferase region with the presumed peptide exit site on the solvent side of the 50 S subunit. The post-transcriptionally modified bases in the 23 S rRNA form a cluster close to the peptidyl transferase area. The minimum conserved core elements of the secondary structure of the 23 S rRNA form a compact block within the 3D structure and, conversely, the points corresponding to the locations of expansion segments in 28 S rRNA all lie on the outside of the structure.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. The 3D arrangement of the double-helical elements of the 23 S and 5 S rRNA molecules in the 50 S subunit. The helices are represented as cylinders, numbered as in Figure 1. The colour-coding is: domain I, red; domain IIa, yellow; domain IIb, orange; domain III, green; domain IV, light blue; domain V, magenta; domain VI, dark blue; and 5 S rRNA grey-brown. (a) View of the structure from the L7/12 side of the subunit. (b) The same view as in (a), but with the layer of helices nearest to the reader removed. (c) View from the L1 side of the subunit. (d) The same view as in (c), but with the outer layer of helices removed as in (b).
Figure 10.
Figure 10. Distribution of the conserved core of the 23 S rRNA in the 50 S subunit. The helices of the conserved core (Figure 9) are displayed as cylinders, numbered and colour-coded as in Figure 3 and Figure 4. The EM density of the 50 S subunit is shown semi-transparent. (a) View from the L7/12 side of the subunit. (b) View from the interface side. (c) View from the L1 side. (d) View from the solvent side.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 298, 35-59) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18936244 H.Ishida, and S.Hayward (2008).
Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome.
  Biophys J, 95, 5962-5973.  
17652323 E.C.Kouvela, G.V.Gerbanas, M.A.Xaplanteri, A.D.Petropoulos, G.P.Dinos, and D.L.Kalpaxis (2007).
Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine.
  Nucleic Acids Res, 35, 5108-5119.  
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
17183511 J.Damborský, M.Petrek, P.Banás, and M.Otyepka (2007).
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles.
  Biotechnol J, 2, 62-67.  
16979906 X.Yan, K.A.Dryden, J.Tang, and T.S.Baker (2007).
Ab initio random model method facilitates 3D reconstruction of icosahedral particles.
  J Struct Biol, 157, 211-225.  
15897324 M.A.Xaplanteri, A.D.Petropoulos, G.P.Dinos, and D.L.Kalpaxis (2005).
Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions.
  Nucleic Acids Res, 33, 2792-2805.  
  17194937 A.Petrov, A.Meskauskas, and J.D.Dinman (2004).
Ribosomal protein L3: influence on ribosome structure and function.
  RNA Biol, 1, 59-65.  
14999102 K.Das, T.Acton, Y.Chiang, L.Shih, E.Arnold, and G.T.Montelione (2004).
Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site.
  Proc Natl Acad Sci U S A, 101, 4041-4046.
PDB code: 1p91
14755567 L.Skibinska, E.Banachowicz, J.GapiƄski, A.Patkowski, and J.Barciszewski (2004).
Structural similarity of E. coli 5S rRNA in solution and within the ribosome.
  Biopolymers, 73, 316-325.  
15139808 S.Subramaniam, and J.L.Milne (2004).
Three-dimensional electron microscopy at molecular resolution.
  Annu Rev Biophys Biomol Struct, 33, 141-155.  
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.
  Biopolymers, 70, 19-41.  
12869709 A.Meskauskas, J.W.Harger, K.L.Jacobs, and J.D.Dinman (2003).
Decreased peptidyltransferase activity correlates with increased programmed -1 ribosomal frameshifting and viral maintenance defects in the yeast Saccharomyces cerevisiae.
  RNA, 9, 982-992.  
15382661 B.Akabayov, A.Henn, M.Elbaum, and I.Sagi (2003).
RNA labeling and immobilization for nano-displacement measurement: probing three-dimensional RNA structure.
  IEEE Trans Nanobioscience, 2, 70-74.  
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.  
11988771 I.D.Campbell (2002).
Timeline: the march of structural biology.
  Nat Rev Mol Cell Biol, 3, 377-381.  
11988472 J.Frank (2002).
Single-particle imaging of macromolecules by cryo-electron microscopy.
  Annu Rev Biophys Biomol Struct, 31, 303-319.  
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.  
11157269 B.M.Fuchs, K.Syutsubo, W.Ludwig, and R.Amann (2001).
In situ accessibility of Escherichia coli 23S rRNA to fluorescently labeled oligonucleotide probes.
  Appl Environ Microbiol, 67, 961-968.  
11120937 B.Vester, and S.Douthwaite (2001).
Macrolide resistance conferred by base substitutions in 23S rRNA.
  Antimicrob Agents Chemother, 45, 1.  
11551941 E.C.Koc, W.Burkhart, K.Blackburn, M.B.Moyer, D.M.Schlatzer, A.Moseley, and L.L.Spremulli (2001).
The large subunit of the mammalian mitochondrial ribosome. Analysis of the complement of ribosomal proteins present.
  J Biol Chem, 276, 43958-43969.  
11511371 I.S.Gabashvili, S.T.Gregory, M.Valle, R.Grassucci, M.Worbs, M.C.Wahl, A.E.Dahlberg, and J.Frank (2001).
The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22.
  Mol Cell, 8, 181-188.  
12762024 J.F.Atkins, P.V.Baranov, O.Fayet, A.J.Herr, M.T.Howard, I.P.Ivanov, S.Matsufuji, W.A.Miller, B.Moore, M.F.Prère, N.M.Wills, J.Zhou, and R.F.Gesteland (2001).
Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression.
  Cold Spring Harb Symp Quant Biol, 66, 217-232.  
11296237 J.Swisher, C.M.Duarte, L.J.Su, and A.M.Pyle (2001).
Visualizing the solvent-inaccessible core of a group II intron ribozyme.
  EMBO J, 20, 2051-2061.  
11713264 M.W.Smith, A.Meskauskas, P.Wang, P.V.Sergiev, and J.D.Dinman (2001).
Saturation mutagenesis of 5S rRNA in Saccharomyces cerevisiae.
  Mol Cell Biol, 21, 8264-8275.  
12762011 P.Sergiev, A.Leonov, S.Dokudovskaya, O.Shpanchenko, O.Dontsova, A.Bogdanov, J.Rinke-Appel, F.Mueller, M.Osswald, K.von Knoblauch, and R.Brimacombe (2001).
Correlating the X-ray structures for halo- and thermophilic ribosomal subunits with biochemical data for the Escherichia coli ribosome.
  Cold Spring Harb Symp Quant Biol, 66, 87.  
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.  
  11780625 V.Ivanov, A.Beniaminov, A.Mikheyev, and E.Minyat (2001).
A mechanism for stop codon recognition by the ribosome: a bioinformatic approach.
  RNA, 7, 1683-1692.  
11297922 V.Ramakrishnan, and P.B.Moore (2001).
Atomic structures at last: the ribosome in 2000.
  Curr Opin Struct Biol, 11, 144-154.  
10998624 E.J.Mancini, and S.D.Fuller (2000).
Supplanting crystallography or supplementing microscopy? A combined approach to the study of an enveloped virus.
  Acta Crystallogr D Biol Crystallogr, 56, 1278-1287.  
11042456 J.Hajdu (2000).
Single-molecule X-ray diffraction.
  Curr Opin Struct Biol, 10, 569-573.  
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.  
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
11080632 R.Brimacombe (2000).
The bacterial ribosome at atomic resolution.
  Structure, 8, R195-R200.  
11042462 Y.Tao, and W.Zhang (2000).
Recent developments in cryo-electron microscopy reconstruction of single particles.
  Curr Opin Struct Biol, 10, 616-622.  
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.