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Title :  DYNAMIC STRUCTURES OF THE L11-RRNA COMPLEX (MDI)
 
Authors :  W. Li, J. Sengupta, B. Rath, J. Frank
Date :  03 Apr 06  (Deposition) - 09 May 06  (Release) - 09 May 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B
Keywords :  L11-Rrna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Li, J. Sengupta, B. Rath, J. Frank
Dynamic Structures Of The L11-Rrna Complex (Mdi)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L11
    Chains: A
    Organism Common: BACTERIA
    Organism Scientific: THERMOTOGA MARITIMA
 
Molecule 2 - RNA (58-MER)
    Chains: B
    Organism Common: BACTERIA
    Organism Scientific: THERMOTOGA MARITIMA
    Other Details: L11 RIBOSOMAL RNA

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2GKY)

(-) Sites  (0, 0)

(no "Site" information available for 2GKY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GKY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GKY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GKY)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L11PS00359 Ribosomal protein L11 signature.RL11_THEMA126-141  1A:119-133

(-) Exons   (0, 0)

(no "Exon" information available for 2GKY)

(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:133
 aligned with RL11_THEMA | P29395 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:133
                                    17        27        37        47        57        67        77        87        97       107       117       127       137   
           RL11_THEMA     8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 140
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee...hhhhhhhhhhh................hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L11   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gky A   1 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain B from PDB  Type:RNA  Length:58
                                                                                          
                 2gky B 134 GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC 191
                                   143       153       163       173       183
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2GKY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GKY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GKY)

(-) Gene Ontology  (9, 9)

Theoretical Model(hide GO term definitions)
Chain A   (RL11_THEMA | P29395)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0070180    large ribosomal subunit rRNA binding    Interacting selectively and non-covalently with the large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0000027    ribosomal large subunit assembly    The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0022625    cytosolic large ribosomal subunit    The large subunit of a ribosome located in the cytosol.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RL11_THEMA | P29395: 1eg0 1ip8 1jqm 1jqs 1jqt 1mms 1mvr 1oln 1pn7 1pn8 1r2w 1r2x 2bcw 2gkz 2jq7 2k3f 487d

(-) Related Entries Specified in the PDB File

2gkz DYNAMIC STRUCTURE OF L11-RRNA COMPLEX (MDII)