3IYR - JenaLib

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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
                                                                                                                                                                                                                                                                                                                                                                                             
                 3iyr 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:143
 aligned with SSRP_THET8 | Q8RR57 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   
           SSRP_THET8     2 APVLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPYEKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGKKAYEKRREDKKEAVRRALEEL 144
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeee......hhhhhhhh.......ee........ee.........................hhhhhhhhhh.......eeeeeeeee.....eeeeeeeee...........hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------SSRP         -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iyr B   2 APVLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPYEKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGKKAYEKRREDKKEAVRRALEEL 144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

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.

Visualization

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Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3iyr)

	Sites
(no "Sites" information available for 3iyr)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3iyr)

Still Images

Databases and Analysis Tools

Databases

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	3iyr
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Description