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(-) Description

Title :  DOCKING OF THE MODIFIED RF2 X-RAY STRUCTURE INTO THE LOW RESOLUTION CRYO-EM MAP OF RF2 E.COLI 70S RIBOSOME
 
Authors :  U. B. S. Rawat, A. V. Zavialov, J. Sengupta, M. Valle, R. A. Grassucci, J. B. Vestergaard, M. Ehrenberg, J. Frank
Date :  22 Aug 02  (Deposition) - 14 Jan 03  (Release) - 01 Feb 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  10.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Rf2, Release Complex, Conformational Changes, Translation, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. B. S. Rawat, A. V. Zavialov, J. Sengupta, M. Valle, R. A. Grassucci, J. Linde, B. Vestergaard, M. Ehrenberg, J. Frank
A Cryo-Electron Microscopic Study Of Ribosome-Bound Termination Factor Rf2
Nature V. 421 87 2003
PubMed-ID: 12511960  |  Reference-DOI: 10.1038/NATURE01224
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE CHAIN RELEASE FACTOR RF-2
    Chains: A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: RELEASE FACTOR 2;
RF2

 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 1MI6)

(-) Sites  (0, 0)

(no "Site" information available for 1MI6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MI6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MI6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_RF2_ECOLI_001 *T246ARF2_ECOLI  ---  ---AA246A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RF_PROK_IPS00745 Prokaryotic-type class I peptide chain release factors signature.RF2_ECOLI245-261  1A:245-261

(-) Exons   (0, 0)

(no "Exon" information available for 1MI6)

(-) 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:362
 aligned with RF2_ECOLI | P07012 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:362
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363  
            RF2_ECOLI     4 INPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEASLKAGL 365
               SCOP domains d1mi6a_ A: 70S ribosome functional complex                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RF_PROK_I        -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mi6 A   4 INPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEASLKAGL 365
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363
   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: Low resolution protein structures (283)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1MI6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1MI6)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RF2_ECOLI | P07012)
molecular function
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0003747    translation release factor activity    Involved in catalyzing the release of a nascent polypeptide chain from a ribosome.
    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: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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  1mi6
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 Related Entries

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

UniProtKB/Swiss-Prot
        RF2_ECOLI | P07012: 1gqe 1ml5 5czp 5dfe 5h5u 5mdv 5mdw 5mgp 5u4i 5u4j 5u9f 5u9g

(-) Related Entries Specified in the PDB File

1dt9 THE CRYSTAL STRUCTURE OF HUMAN EUKARYOTIC RELEASE FACTOR ERF1 RELATED ID: EMD-1006 RELATED DB: EMDB RELATED ID: EMD-1007 RELATED DB: EMDB RELATED ID: EMD-1008 RELATED DB: EMDB RELATED ID: EMD-1009 RELATED DB: EMDB RELATED ID: EMD-1010 RELATED DB: EMDB
1gqe POLYPEPTIDE CHAIN RELEASE FACTOR 2 (RF2) FROM E. COLI