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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOSOME RECYCLING FACTOR FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  H. Nakano, Y. Yamaichi, S. Uchiyama, T. Yoshida, K. Nishina, H. Kato, T. Ohkubo, T. Honda, Y. Yamagata, Y. Kobayashi
Date :  05 Nov 01  (Deposition) - 17 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Nakano, T. Yoshida, S. Uchiyama, M. Kawachi, H. Matsuo, T. Kato, A. Ohshima, Y. Yamaichi, T. Honda, H. Kato, Y. Yamagata, T. Ohkubo, Y. Kobayashi
Structure And Binding Mode Of A Ribosome Recycling Factor (Rrf) From Mesophilic Bacterium
J. Biol. Chem. V. 278 3427 2003
PubMed-ID: 12411440  |  Reference-DOI: 10.1074/JBC.M208098200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOME RECYCLING FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 670

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1IS1)

(-) Sites  (0, 0)

(no "Site" information available for 1IS1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IS1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IS1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IS1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IS1)

(-) Exons   (0, 0)

(no "Exon" information available for 1IS1)

(-) 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_VIBPA | Q8GRF5 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_VIBPA     1 MINEIKKDAQERMDKSVEALKNNLSKVRTGRAHPSLLSGISVEYYGAATPLNQVANVVAEDARTLAITVFDKELTQKVEKAIMMSDLGLNPMSAGTIIRVPLPPLTEERRKDLVKIVRGEAEGGRVAVRNIRRDANNDLKALLKDKEISEDEDRKAQEEIQKLTDVAVKKIDEVLAAKEKELMEV 185
               SCOP domains d1is1a_ A: Ribosome recycling factor, RRF                                                                                                                                                 SCOP domains
               CATH domains -1is1A01 A:2-30,A:106-185     1is1A02 A:31-105  [code=3.30.1360.40, no name defined]                     1is1A01 A:2-30,A:106-185  [code=1.10.132.20, no name defined]                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..eeee..eeee....eeeeeee..eeeeee....hhhhhhhhhhhh......eee..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1is1 A   1 MINEIKKDAQERMDKSVEALKNNLSKVRTGRAHPSLLSGISVEYYGAATPLNQVANVVAEDARTLAITVFDKELTQKVEKAIMMSDLGLNPMSAGTIIRVPLPPLTEERRKDLVKIVRGEAEGGRVAVRNIRRDANNDLKALLKDKEISEDEDRKAQEEIQKLTDVAVKKIDEVLAAKEKELMEV 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IS1)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RRF_VIBPA | Q8GRF5)
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.
    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.

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 Related Entries

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