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(-) Description

Title :  DOCKING OF THE MODIFIED RF3 X-RAY STRUCTURE INTO CRYO-EM MAP OF E.COLI 70S RIBOSOME BOUND WITH RF3
 
Authors :  H. Gao, Z. Zhou, U. Rawat, C. Huang, L. Bouakaz, C. Wang, Y. Liu, A. Zavialov, R. Gursky, S. Sanyal, M. Ehrenberg, J. Frank, H. Song
Date :  27 Nov 06  (Deposition) - 24 Jul 07  (Release) - 02 Feb 10  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  15.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Rf3, Ribosome, Cryo-Em, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Gao, Z. Zhou, U. Rawat, C. Huang, L. Bouakaz, C. Wang, Z. Cheng, Y. Liu, A. Zavialov, R. Gursky, S. Sanyal, M. Ehrenberg, J. Frank, H. Song
Rf3 Induces Ribosomal Conformational Changes Responsible For Dissociation Of Class I Release Factors
Cell(Cambridge, Mass. ) V. 129 929 2007
PubMed-ID: 17540173  |  Reference-DOI: 10.1016/J.CELL.2007.03.050

(-) Compounds

Molecule 1 - PEPTIDE CHAIN RELEASE FACTOR 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RF-3

 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 2O0F)

(-) Sites  (0, 0)

(no "Site" information available for 2O0F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O0F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O0F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O0F)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.RF3_ECOLI58-73  1A:70-73

(-) Exons   (0, 0)

(no "Exon" information available for 2O0F)

(-) 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:488
 aligned with RF3_ECOLI | P0A7I4 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:527
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       
            RF3_ECOLI     3 LSPYLQEVAKRRTFAIISHPDAGKTTITEKVLLFGQAIQTAGTVKGRGSNQHAKSDWMEMEKQRGISITTSVMQFPYHDCLVNLLDTPGHEDFSEDTYRTLTAVDCCLMVIDAAKGVEDRTRKLMEVTRLRDTPILTFMNKLDRDIRDPMELLDEVENELKIGCAPITWPIGCGKLFKGVYHLYKDETYLYQSGKGHTIQEVRIVKGLNNPDLDAAVGEDLAQQLRDELELVKGASNEFDKELFLAGEITPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMKLRQVRTAKDVVISDALTFMAGDRSHVEEAYPGDILGLHNHGTIQIGDTFTQGEMMKFTGIPNFAPELFRRIRLKDPLKQKQLLKGLVQLSEEGAVQVFRPISNNDLIVGAVGVLQFDVVVARLKSEYNVEAVYESVNVATARWVECADAKKFEEFKRKNESQLALDGGDNLAYIATSMVNLRLAQERYPDVQFHQTREH 529
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................-------------------------------.........................................................................................................................................................................................................................................................................................-----...................................................---........................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o0f A   3 LSPYLQEVAKRRTFAIISHPDAGKTTITEKVLLFGQ-------------------------------ITTSVMQFPYHDCLVNLLDTPGHEDFSEDTYRTLTAVDCCLMVIDAAKGVEDRTRKLMEVTRLRDTPILTFMNKLDRDIRDPMELLDEVENELKIGCAPITWPIGCGKLFKGVYHLYKDETYLYQSGKGHTIQEVRIVKGLNNPDLDAAVGEDLAQQLRDELELVKGASNEFDKELFLAGEITPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMKLRQVRTAKDVVISDALTFMA-----VEEAYPGDILGLHNHGTIQIGDTFTQGEMMKFTGIPNFAPELFRRIRLKDP---KQLLKGLVQLSEEGAVQVFRPISNNDLIVGAVGVLQFDVVVARLKSEYNVEAVYESVNVATARWVECADAKKFEEFKRKNESQLALDGGDNLAYIATSMVNLRLAQERYPDVQFHQTREH 529
                                    12        22        32     |   -         -         -       |72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       | -   |   362       372       382       392       402   |   412       422       432       442       452       462       472       482       492       502       512       522       
                                                              38                              70                                                                                                                                                                                                                                                                                     350   356                                               406 410
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 2O0F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O0F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O0F)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RF3_ECOLI | P0A7I4)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016150    translation release factor activity, codon nonspecific    A translation release factor that is not specific to particular codons; binds to guanine nucleotides.
    GO:0016149    translation release factor activity, codon specific    A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.
biological process
    GO:0006449    regulation of translational termination    Any process that modulates the frequency, rate or extent of translational termination.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RF3_ECOLI | P0A7I4: 2h5e 4v85 4v89 4v8o

(-) Related Entries Specified in the PDB File

2h5e CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE RELEASE FACTOR RF3 RELATED ID: EMD-1302 RELATED DB: EMDB