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(-) Description

Title :  TMRNA-SMPB: A JOURNEY TO THE CENTER OF THE BACTERIAL RIBOSOME
 
Authors :  F. Weis, P. Bron, E. Giudice, J. P. Rolland, D. Thomas, B. Felden, R. Gill
Date :  16 Apr 10  (Deposition) - 20 Oct 10  (Release) - 01 Dec 10  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  13.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tmrna, Smpb, Ribosome, Trans-Translation, Ribosomal Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Weis, P. Bron, E. Giudice, J. P. Rolland, D. Thomas, B. Felden, R. Gillet
Tmrna-Smpb: A Journey To The Centre Of The Bacterial Ribosome.
Embo J. V. 29 3810 2010
PubMed-ID: 20953161  |  Reference-DOI: 10.1038/EMBOJ.2010.252

(-) Compounds

Molecule 1 - TMRNA
    Chains: A
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
 
Molecule 2 - SSRA-BINDING PROTEIN
    Chains: B
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3IYQ)

(-) Sites  (0, 0)

(no "Site" information available for 3IYQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IYQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IYQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IYQ)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SSRPPS01317 SsrA-binding protein.SSRP_THET822-34  1B:22-34

(-) Exons   (0, 0)

(no "Exon" information available for 3IYQ)

(-) 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:RNA  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
                 3iyq A   1 GGGGGUGAAACGGUCUCGACGGGGGUCGCCGAGGGCGUGGCUGCGCGCCGAGGUGCGGGUGGCCUCGUAAAAACCCGCAACGGCAUAACUGCCAACACCAACUACGCUCUCGCGGCUUAAUGACCGCGACCUCGCCCGGUAGCCCUGCCGGGGGCUCACCGGAAGCGGGGACACAAACCCGGCUAGCCCGGGGCCACGCCCUCUAACCCCGGGCGAAGCUUGAAGGGGGCUCGCUCCUGGCCGCCCGUCCGCGGGCCAAGCCAGGAGGACACGCGAAACGCGGACUACGCGCGUAGAGGCCCGCCGUAGGGACCUUCGGACGGGGGUUCGACUCCCCCCACCUCCACCA 349
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with SSRP_THET8 | Q8RR57 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:122
                                    11        21        31        41        51        61        71        81        91       101       111       121  
           SSRP_THET8     2 APVLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPYEKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGK 123
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee...hhhhhhhhhhh.......eee......eee....................ee...hhhhhh.hhhhhhhh..eeeeeeeee.....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------SSRP         ----------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iyq B   2 APVLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPYEKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGK 123
                                    11        21        31        41        51        61        71        81        91       101       111       121
   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  (0, 0)

(no "SCOP Domain" information available for 3IYQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IYQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IYQ)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (SSRP_THET8 | Q8RR57)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
biological process
    GO:0070929    trans-translation    A translational elongation process in which transfer of a translating ribosome from one mRNA to another RNA template takes place. Trans-translation occurs during tmRNA release of stalled ribosomes.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3iyq
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  SSRP_THET8 | Q8RR57
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 Related Entries

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

UniProtKB/Swiss-Prot
        SSRP_THET8 | Q8RR57: 1j1h 1wjx 2czj 3iyr 3iz4 4v6t 4v8q

(-) Related Entries Specified in the PDB File

3iyr