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(-) Description

Title :  COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM MAP OF THE 70S RIBOSOME
 
Authors :  M. Valle, A. Zavialov, W. Li, S. M. Stagg, J. Sengupta, R. C. Nielsen, P. Nissen, S. C. Harvey, M. Ehrenberg, J. Frank
Date :  30 Sep 03  (Deposition) - 04 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  9.00
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Rna, Ribosomal Protein, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Valle, A. Zavialov, W. Li, S. M. Stagg, J. Sengupta, R. C. Nielsen, P. Nissen, S. C. Harvey, M. Ehrenberg, J. Frank
Incorporation Of Aminoacyl-Trna Into The Ribosome As Seen By Cryo-Electron Microscopy
Nat. Struct. Biol. V. 10 899 2003
PubMed-ID: 14566331  |  Reference-DOI: 10.1038/NSB1003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 58NTS OF 23S RRNA
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 50S RIBOSOMAL PROTEIN L11
    Chains: A
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1R2W)

(-) Sites  (0, 0)

(no "Site" information available for 1R2W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R2W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R2W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R2W)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L11PS00359 Ribosomal protein L11 signature.RL11_THEMA126-141  1A:120-134

(-) Exons   (0, 0)

(no "Exon" information available for 1R2W)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:134
 aligned with RL11_THEMA | P29395 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:134
                                                                                             73                                                                   
                                                                                           72 |                                                                   
                                    17        27        37        47        57        67    | | 76        86        96       106       116       126       136    
           RL11_THEMA     8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKT-PPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 140
               SCOP domains d1r2wa_ A: 70S ribosome functional complex                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L11   PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r2w A   1 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTEPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain C from PDB  Type:RNA  Length:57
                                                                                         
                 1r2w C   1 CUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC  57
                                    10        20        30        40        50
   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Low resolution protein structures (283)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R2W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1R2W)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(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 1r2x 2bcw 2gky 2gkz 2jq7 2k3f 487d

(-) Related Entries Specified in the PDB File

1ffk CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI AT 2.4 ANGSTROM RESOLUTION
1qzb COORDINATES OF THE A-SITE TRNA MODEL FITTED INTO THE CRYO- EM MAP OF 70S RIBOSOME IN THE PRE-TRANSLOCATIONAL STATE
1qzc COORDINATES OF S12, SH44, LH69 AND SRL SEPARATELY FITTED INTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME
1qzd EF-TU.KIRROMYCIN COORDINATES FITTED INTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME
1r2x COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME RELATED ID: EMD-1056 RELATED DB: EMDB