spacer
spacer

PDBsum entry 1dfu

Go to PDB code: 
protein dna_rna metals links
Ribosome PDB id
1dfu
Jmol
Contents
Protein chain
94 a.a. *
DNA/RNA
Metals
_MG ×5
Waters ×242
* Residue conservation analysis
PDB id:
1dfu
Name: Ribosome
Title: Crystal structure of e.Coli ribosomal protein l25 complexed with a 5s rrna fragment at 1.8 a resolution
Structure: 5s rrna. Chain: m. Fragment: loop e-helix iv fragment. Engineered: yes. Other_details: a fragment of 5s rrna in 50s ribosomal subunit. 5s rrna. Chain: n. Fragment: loop e-helix iv fragment.
Source: Synthetic: yes. Other_details: this sequence occurs naturally in e.Coli. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
1.80Å     R-factor:   0.207     R-free:   0.225
Authors: M.Lu,T.A.Steitz
Key ref:
M.Lu and T.A.Steitz (2000). Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution. Proc Natl Acad Sci U S A, 97, 2023-2028. PubMed id: 10696113 DOI: 10.1073/pnas.97.5.2023
Date:
21-Nov-99     Release date:   02-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25
Seq:
Struc:
94 a.a.
94 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     4 terms  

 

 
DOI no: 10.1073/pnas.97.5.2023 Proc Natl Acad Sci U S A 97:2023-2028 (2000)
PubMed id: 10696113  
 
 
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
M.Lu, T.A.Steitz.
 
  ABSTRACT  
 
The crystal structure of Escherichia coli ribosomal protein L25 bound to an 18-base pair portion of 5S ribosomal RNA, which contains "loop E," has been determined at 1.8-A resolution. The protein primarily recognizes a unique RNA shape, although five side chains make direct or water-mediated interactions with bases. Three beta-strands lie in the widened minor groove of loop E formed by noncanonical base pairs and cross-strand purine stacks, and an alpha-helix interacts in an adjacent widened major groove. The structure of loop E is largely the same as that of uncomplexed RNA (rms deviation of 0.4 A for 11 base pairs), and 3 Mg(2+) ions that stabilize the noncanonical base pairs lie in the same or similar locations in both structures. Perhaps surprisingly, those residues interacting with the RNA backbone are the most conserved among known L25 sequences, whereas those interacting with the bases are not.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. The three Mg2+ ions bound in the minor groove of loop E are shown as they occur in the L25 complex in A and in the uncomplexed RNA in B. The positions of Mg2+ ions C and D are identical in both, and the position of B is similar.
Figure 4.
Fig. 4. Base-specific interactions in the minor groove. The observed direct or water-mediated interactions between the protein and three base pairs are shown in A-C, whereas the lack of interaction expected if GC or AU base pairs were substituted is shown in D-F.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20397215 J.Sheng, and Z.Huang (2010).
Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies.
  Chem Biodivers, 7, 753-785.  
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.  
18298371 A.V.Korobeinikova, G.M.Gongadze, A.P.Korepanov, B.D.Eliseev, M.V.Bazhenova, and M.B.Garber (2008).
5S rRNA-recognition module of CTC family proteins and its evolution.
  Biochemistry (Mosc), 73, 156-163.  
18160411 N.J.Reiter, L.J.Maher, and S.E.Butcher (2008).
DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer.
  Nucleic Acids Res, 36, 1227-1236.
PDB code: 2jwv
17605815 A.M.Burroughs, S.Balaji, L.M.Iyer, and L.Aravind (2007).
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.
  Biol Direct, 2, 18.  
17526525 D.Xu, T.Landon, N.L.Greenbaum, and M.O.Fenley (2007).
The electrostatic characteristics of G.U wobble base pairs.
  Nucleic Acids Res, 35, 3836-3847.  
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.  
17169989 J.Jiang, J.Sheng, N.Carrasco, and Z.Huang (2007).
Selenium derivatization of nucleic acids for crystallography.
  Nucleic Acids Res, 35, 477-485.
PDB codes: 1z7i 2dlj 2gpx 2h05
17407165 K.S.Sandhu, and D.Dash (2007).
Dynamic alpha-helices: conformations that do not conform.
  Proteins, 68, 109-122.  
16604424 B.Bardiaux, T.E.Malliavin, M.Nilges, and A.K.Mazur (2006).
Comparison of different torsion angle approaches for NMR structure determination.
  J Biomol NMR, 34, 153-166.  
16478715 G.S.Couch, D.K.Hendrix, and T.E.Ferrin (2006).
Nucleic acid visualization with UCSF Chimera.
  Nucleic Acids Res, 34, e29.  
17021109 M.Mueller, S.Bunk, I.Diterich, M.Weichel, C.Rauter, D.Hassler, C.Hermann, R.Crameri, and T.Hartung (2006).
Identification of Borrelia burgdorferi ribosomal protein L25 by the phage surface display method and evaluation of the protein's value for serodiagnosis.
  J Clin Microbiol, 44, 3778-3780.  
17139090 S.Tishchenko, E.Nikonova, A.Nikulin, N.Nevskaya, S.Volchkov, W.Piendl, M.Garber, and S.Nikonov (2006).
Structure of the ribosomal protein L1-mRNA complex at 2.1 A resolution: common features of crystal packing of L1-RNA complexes.
  Acta Crystallogr D Biol Crystallogr, 62, 1545-1554.
PDB code: 2hw8
15580277 B.L.Golden, H.Kim, and E.Chase (2005).
Crystal structure of a phage Twort group I ribozyme-product complex.
  Nat Struct Mol Biol, 12, 82-89.
PDB code: 1y0q
15784587 H.Stoll, J.Dengjel, C.Nerz, and F.Götz (2005).
Staphylococcus aureus deficient in lipidation of prelipoproteins is attenuated in growth and immune activation.
  Infect Immun, 73, 2411-2423.  
15339800 K.Réblová, N.Spacková, J.Koca, N.B.Leontis, and J.Sponer (2004).
Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.
  Biophys J, 87, 3397-3412.  
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.  
14523911 B.Fürtig, C.Richter, J.Wöhnert, and H.Schwalbe (2003).
NMR spectroscopy of RNA.
  Chembiochem, 4, 936-962.  
12824344 H.Yang, F.Jossinet, N.Leontis, L.Chen, J.Westbrook, H.Berman, and E.Westhof (2003).
Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
12770867 K.Réblová, N.Spacková, R.Stefl, K.Csaszar, J.Koca, N.B.Leontis, and J.Sponer (2003).
Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.
  Biophys J, 84, 3564-3582.  
12837388 P.Auffinger, L.Bielecki, and E.Westhof (2003).
The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations.
  Chem Biol, 10, 551-561.  
12513990 R.Gardan, O.Duché, S.Leroy-Sétrin, and J.Labadie (2003).
Role of ctc from Listeria monocytogenes in osmotolerance.
  Appl Environ Microbiol, 69, 154-161.  
11752286 M.Szymanski, M.Z.Barciszewska, V.A.Erdmann, and J.Barciszewski (2002).
5S Ribosomal RNA Database.
  Nucleic Acids Res, 30, 176-178.  
11418764 R.Fedorov, V.Meshcheryakov, G.Gongadze, N.Fomenkova, N.Nevskaya, M.Selmer, M.Laurberg, O.Kristensen, S.Al-Karadaghi, A.Liljas, M.Garber, and S.Nikonov (2001).
Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins.
  Acta Crystallogr D Biol Crystallogr, 57, 968-976.
PDB code: 1feu
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.  
11350033 T.Nakashima, M.Yao, S.Kawamura, K.Iwasaki, M.Kimura, and I.Tanaka (2001).
Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.
  RNA, 7, 692-701.
PDB code: 1iq4
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
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.  
11073218 R.Klinck, E.Westhof, S.Walker, M.Afshar, A.Collier, and F.Aboul-Ela (2000).
A potential RNA drug target in the hepatitis C virus internal ribosomal entry site.
  RNA, 6, 1423-1431.
PDB code: 1fqz
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.