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PDBsum entry 1y39

Go to PDB code: 
protein dna_rna ligands metals links
Structural protein/RNA PDB id
1y39
Jmol PyMol
Contents
Protein chains
74 a.a. *
DNA/RNA
Ligands
GOL ×2
Metals
3CO ×2
__K ×2
_MG ×18
Waters ×15
* Residue conservation analysis
PDB id:
1y39
Name: Structural protein/RNA
Title: Co-evolution of protein and RNA structures within a highly c ribosomal domain
Structure: 58 nucleotide ribosomal 23s RNA domain. Chain: c, d. Engineered: yes. Mutation: yes. 50s ribosomal protein l11. Chain: a, b. Fragment: c-terminal domain of ribosomal protein l11. Synonym: ribosomal protein l11. Engineered: yes.
Source: Synthetic: yes. Other_details: nts 1051-1108 from e. Coli 23s rrna. Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.220     R-free:   0.253
Authors: M.S.Dunstan,D.Guhathakurta,D.E.Draper,G.L.Conn
Key ref:
M.S.Dunstan et al. (2005). Coevolution of protein and RNA structures within a highly conserved ribosomal domain. Chem Biol, 12, 201-206. PubMed id: 15734647 DOI: 10.1016/j.chembiol.2004.11.019
Date:
24-Nov-04     Release date:   22-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P56210  (RL11_GEOSE) -  50S ribosomal protein L11 (Fragment)
Seq:
Struc:
133 a.a.
74 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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

 

 
DOI no: 10.1016/j.chembiol.2004.11.019 Chem Biol 12:201-206 (2005)
PubMed id: 15734647  
 
 
Coevolution of protein and RNA structures within a highly conserved ribosomal domain.
M.S.Dunstan, D.Guhathakurta, D.E.Draper, G.L.Conn.
 
  ABSTRACT  
 
The X-ray crystal structure of a ribosomal L11-rRNA complex with chloroplast-like mutations in both protein and rRNA is presented. The global structure is almost identical to that of the wild-type (bacterial) complex, with only a small movement of the protein alpha helix away from the surface of the RNA required to accommodate the altered protein residue. In contrast, the specific hydrogen bonding pattern of the mutated residues is substantially different, and now includes a direct interaction between the protein side chain and an RNA base edge and a water-mediated contact. Comparison of the two structures allows the observations of sequence variation and relative affinities of wild-type and mutant complexes to be clearly rationalized, but reinforces the concept that there is no single simple code for protein-RNA recognition.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Secondary and Tertiary Structures of the 58 Nucleotide L11 Binding Domain rRNA
Figure 3.
Figure 3. Interactions in the Ch-like rRNA-L11(C76) Complex
 
  The above figures are reprinted by permission from Cell Press: Chem Biol (2005, 12, 201-206) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19369248 M.S.Dunstan, P.C.Hang, N.V.Zelinskaya, J.F.Honek, and G.L.Conn (2009).
Structure of the Thiostrepton Resistance Methyltransferase{middle dot}S-Adenosyl-L-methionine Complex and Its Interaction with Ribosomal RNA.
  J Biol Chem, 284, 17013-17020.
PDB code: 3gyq
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.

 

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