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(-) Description

Title :  COORDINATES OF S12, SH44, LH69 AND SRL SEPARATELY FITTED INTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 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 :  16 Sep 03  (Deposition) - 04 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  9.00
Chains :  Asym./Biol. Unit :  A,B,C,L
Keywords :  Ribosomal Protein, Rrna, 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 - 16S RRNA
    Chains: A
    Fragment: HELIX 44
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MRE 600
 
Molecule 2 - 23S RRNA
    Chains: B
    Fragment: HELIX 69
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MRE 600
 
Molecule 3 - 23S RRNA
    Chains: C
    Fragment: SARCIN/RICIN LOOP (SRL)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MRE 600
 
Molecule 4 - 30S RIBOSOMAL PROTEIN S12
    Chains: L
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1QZC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S12PS00055 Ribosomal protein S12 signature.RS12_THET843-50  1L:42-49

(-) Exons   (0, 0)

(no "Exon" information available for 1QZC)

(-) 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:44
                                                                            
                 1qzc A   1 CGCCCGUCACGCCAUGGGAGCGUGACUGGGGCGAAGUCGUAACA  44
                                    10        20        30        40    


Chain B from PDB  Type:RNA  Length:20
                                                    
                 1qzc B   2 GGCCGUAACUAUAACGGUCC  21
                                    11        21


Chain C from PDB  Type:RNA  Length:27
                                                           
                 1qzc C   1 GACCGUAUAGUACGAGAGGAACUACGG  27
                                    10        20       


Chain L from PDB  Type:PROTEIN  Length:124
 aligned with RS12_THET8 | Q5SHN3 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
           RS12_THET8     2 PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEA 125
               SCOP domains d1qzcl_ L: 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 -----------------------------------------RIBOSOMA--------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qzc L   1 PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEA 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (RS12_THET8 | Q5SHN3)
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.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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.
    GO:0015935    small ribosomal subunit    The smaller of the two subunits of a ribosome.

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  1qzc
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  RS12_THET8 | Q5SHN3
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 Related Entries

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

UniProtKB/Swiss-Prot
        RS12_THET8 | Q5SHN3: 1fjg 1hnw 1hnx 1hnz 1hr0 1i94 1i95 1i96 1i97 1ibk 1ibl 1ibm 1j5e 1jgo 1jgp 1jgq 1l1u 1ml5 1mvr 1n32 1n33 1n34 1n36 1pn7 1pn8 1vvj 1vy4 1vy5 1vy6 1vy7 1xmo 1xmq 1xnq 1xnr 2e5l 2f4v 2hhh 2uu9 2uua 2uub 2uuc 2uxb 2uxc 2uxd 2vqe 2vqf 2zm6 3oto 3t1h 3t1y 4aqy 4b3m 4b3r 4b3s 4b3t 4duy 4duz 4dv0 4dv1 4dv2 4dv3 4dv4 4dv5 4dv6 4dv7 4gkj 4gkk 4ji0 4ji1 4ji2 4ji3 4ji4 4ji5 4ji6 4ji7 4ji8 4jv5 4jya 4k0k 4khp 4l47 4l71 4lel 4lfz 4lnt 4lsk 4lt8 4ox9 4p6f 4p70 4tua 4tub 4tuc 4tud 4tue 4v42 4v49 4v4a 4v4i 4v4p 4v4r 4v4s 4v4t 4v4x 4v4y 4v4z 4v51 4v5a 4v5c 4v5d 4v5e 4v5f 4v5g 4v5j 4v5k 4v5l 4v5m 4v5n 4v5p 4v5q 4v5r 4v5s 4v68 4v6a 4v6f 4v6g 4v7j 4v7k 4v7l 4v7m 4v7w 4v7x 4v7y 4v7z 4v87 4v8a 4v8b 4v8c 4v8d 4v8e 4v8f 4v8g 4v8h 4v8i 4v8j 4v8n 4v8o 4v8q 4v8u 4v8x 4v90 4v95 4v97 4v9a 4v9b 4v9h 4v9i 4v9r 4v9s 4w2e 4w2f 4w2g 4w2h 4w2i 4w4g 4wpo 4wq1 4wqf 4wqr 4wqu 4wqy 4wr6 4wra 4wro 4wsd 4wsm 4wt1 4wt8 4wu1 4wzd 4wzo 4x62 4x64 4x65 4x66 4y4o 4y4p 4yhh 4ypb 4yy3 4yzv 4z3s 4z8c 4zer 4zsn 5a9z 5aa0 5br8 5czp 5d8b 5dfe 5dox 5doy 5e7k 5e81 5el4 5el5 5el6 5el7 5f8k 5fdu 5fdv 5hau 5hcp 5hcq 5hcr 5hd1 5ib7 5ib8 5ibb 5imq 5imr 5iwa 5j30 5j3c 5j4b 5j4c 5j8b 5lmn 5lmo 5lmp 5lmq 5lmr 5lms 5lmt 5lmu 5lmv

(-) Related Entries Specified in the PDB File

1ffk CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI AT 2.4 ANGSTROM RESOLUTION
1ibm STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE
1qza COORDINATES OF THE A/T SITE TRNA MODEL FITTED INTO THE CRYO -EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME
1qzb COORDINATES OF THE A-SITE TRNA MODEL FITTED INTO THE CRYO- EM MAP OF 70S RIBOSOME IN THE PRE-TRANSLOCATIONAL STATE
1qzd EF-TU.KIRROMYCIN COORDINATES FITTED INTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME
1r2w COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM MAP OF THE 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