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(-) Description

Title :  COORDINATES OF RRF FITTED INTO CRYO-EM MAP OF THE 70S POST-TERMINATION COMPLEX
 
Authors :  N. Gao, A. V. Zavialov, W. Li, J. Sengupta, M. Valle, R. P. Gursky, M. Ehrenberg, J. Frank
Date :  11 May 05  (Deposition) - 14 Jun 05  (Release) - 02 Feb 10  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  14.10
Chains :  Asym./Biol. Unit :  A,B,C,L
Keywords :  Ribosome Recycling Factor, Elongation Factor G, 70S, Post- Termination Complex, Biosynthetic/Structural Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Gao, A. V. Zavialov, W. Li, J. Sengupta, M. Valle, R. P. Gursky, M. Ehrenberg, J. Frank
Mechanism For The Disassembly Of The Posttermination Complex Inferred From Cryo-Em Studies.
Mol. Cell V. 18 663 2005
PubMed-ID: 15949441  |  Reference-DOI: 10.1016/J.MOLCEL.2005.05.005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL 23S RNA
    ChainsB
    FragmentFRAGMENT OF LARGE SUBUNIT RRNA HELIX 69-71
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - RIBOSOMAL 16S RNA
    ChainsC
    FragmentFRAGMENT OF SMALL SUBUNIT RRNA HELIX 44
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 3 - RIBOSOME RECYCLING FACTOR
    ChainsA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymRIBOSOME RELEASING FACTOR, RRF
 
Molecule 4 - 30S RIBOSOMAL PROTEIN S12
    ChainsL
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 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 1ZN1)

(-) Sites  (0, 0)

(no "Site" information available for 1ZN1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZN1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZN1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_RS12_ECOLI_001 *K43RRS12_ECOLI  ---  ---LK42R
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S12PS00055 Ribosomal protein S12 signature.RS12_ECOLI43-50  1L:42-49

(-) Exons   (0, 0)

(no "Exon" information available for 1ZN1)

(-) 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:185
 aligned with RRF_ECOLI | P0A805 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
           RRF_ECOLI      1 MISDIRKDAEVRMDKCVEAFKTQISKIRTGRASPSLLDGIVVEYYGTPTPLRQLASVTVEDSRTLKINVFDRSMSPAVEKAIMASDLGLNPNSAGSDIRVPLPPLTEERRKDLTKIVRGEAEQARVAVRNVRRDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAELMQF  185
               SCOP domains d1zn1a1 A:1-185 Ribosome recycling factor, RRF                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zn1 A    1 MISDIRKDAEVRMDKCVEAFKTQISKIRTGRASPSLLDGIVVEYYGTPTPLRQLASVTVEDSRTLKINVFDRSMSPAVEKAIMASDLGLNPNSAGSDIRVPLPPLTEERRKDLTKIVRGEAEQARVAVRNVRRDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAELMQF  185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     

Chain B from PDB  Type:RNA  Length:59
                                                                                            
                1zn1 B 1906 GGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUG 1964
                                  1915      1925      1935      1945      1955         

Chain C from PDB  Type:RNA  Length:40
                                                                         
                1zn1 C 1405 GUCACACCAUGGGAGUGGGUAUUCAUGACUGGGGUGAAGU 1495
                                  1414      1424|     1485      1495
                                            1424|                   
                                             1476                   

Chain L from PDB  Type:PROTEIN  Length:97
 aligned with RS12_ECOLI | P0A7S3 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:97
                                    37        47        57        67        77        87        97       107       117       
          RS12_ECOLI     28 PQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA  124
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------R--------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------RIBOSOMA-------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                1zn1 L   27 PQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA  123
                                    36        46        56        66        76        86        96       106       116       

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZN1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZN1)

(-) Gene Ontology  (21, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RRF_ECOLI | P0A805)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043023    ribosomal large subunit binding    Interacting selectively and non-covalently with any part of the larger ribosomal subunit.
biological process
    GO:0002184    cytoplasmic translational termination    The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon.
    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.
    GO:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain L   (RS12_ECOLI | P0A7S3)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0034336    misfolded RNA binding    Interacting selectively and non-covalently with an RNA molecule that has assumed an incorrect conformation.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0000372    Group I intron splicing    The splicing of Group I introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group I introns and involved in determining the locations of the splice sites (there do not appear to be consensus splice site sequences) as well as having a role in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions, generally with exogenous guanosine as the initiating nucleophile. The intron is excised as a linear piece (though it may subsequently circularize).
    GO:0034337    RNA folding    The process of assisting in the covalent and noncovalent assembly of single or multimeric RNAs into the correct tertiary structure.
    GO:0033120    positive regulation of RNA splicing    Any process that activates or increases the frequency, rate or extent of RNA splicing.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0022627    cytosolic small ribosomal subunit    The small subunit of a ribosome located in the cytosol.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        RRF_ECOLI | P0A8051ek8 1ise 1y69 1zn0 2rdo 4v9c 4v9d 4woi
        RS12_ECOLI | P0A7S31m5g 1mj1 2ykr 3deg 3ep2 3eq3 3eq4 3iy8 3j0d 3j0e 3j9y 3j9z 3ja1 3jbu 3jbv 3jcd 3jce 3jcj 3jcn 4a2i 4adv 4u1u 4u1v 4u20 4u24 4u25 4u26 4u27 4v47 4v48 4v4h 4v4q 4v4v 4v4w 4v50 4v52 4v53 4v54 4v55 4v56 4v57 4v5b 4v5h 4v5y 4v64 4v65 4v66 4v69 4v6c 4v6d 4v6e 4v6k 4v6l 4v6m 4v6n 4v6o 4v6p 4v6q 4v6r 4v6s 4v6t 4v6v 4v6y 4v6z 4v70 4v71 4v72 4v73 4v74 4v75 4v76 4v77 4v78 4v79 4v7a 4v7b 4v7c 4v7d 4v7i 4v7s 4v7t 4v7u 4v7v 4v85 4v89 4v9c 4v9d 4v9o 4v9p 4wf1 4woi 4www 4ybb 5afi 5h5u 5iqr 5it8 5j5b 5j7l 5j88 5j8a 5j91 5jc9 5jte 5ju8 5kcr 5kcs 5kps 5kpv 5kpw 5kpx 5l3p 5lza 5lzb 5lzc 5lzd 5lze 5lzf 5mdv 5mdw 5mdy 5mdz 5me0 5me1 5mgp 5my1 5no2 5no3 5no4 5u4i 5u4j

(-) Related Entries Specified in the PDB File

1ek8 RRF STRUCTURE FROM E.COLI
1p6g 30S SUBUNIT
1p85 50S SUBUNIT
1zn0 RELATED ID: EMD-1127 RELATED DB: EMDB RELATED ID: EMD-1128 RELATED DB: EMDB