DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dent-2013-1 ecolx Escherichia coli 3d-em 3D electron microscopy 3D-EM electron tomog predetermined predetermined participant predetermined Dent KC., Thompson R., Barker AM., Hiscox JA., Barr JN., Stockley PG., Ranson NA. DIP original experiment: DIP-255710X Structure (London, England : 1993) 2013 IMEx The asymmetric structure of an icosahedral virus bound to its receptor suggests a mechanism for genome release. Dent KC., Thompson R., Barker AM., Hiscox JA., Barr JN., Stockley PG., Ranson NA. Only protein-protein interactions imex curation borodavka-2012-1 ecolx Escherichia coli tem transmission electron microscopy tem predetermined predetermined participant predetermined Borodavka A., Tuma R., Stockley PG. DIP original experiment: DIP-253605X Proceedings of the National Academy of Sciences of the United States of America 2012 IMEx Evidence that viral RNAs have evolved for efficient, two-stage packaging. Borodavka A., Tuma R., Stockley PG. Only protein-protein interactions imex curation capsd_bpms2 Capsid protein Coat protein protein protein bpms2 Enterobacteria phage MS2 MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY capsd_bpms2-1 3255285 N/A 3255286 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false capsd_bpms2-2 3245201 N/A 3255286 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ shtatland-2000-1 Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX. in vitro In vitro selex systematic evolution of ligands by exponential enrichment in vitro evolution of nucleic acids selex full dna sequence full identification by DNA sequencing full dna sequence Shtatland T., Gill SC., Javornik BE., Johansson HE., Singer BS., Uhlenbeck OC., Zichi DA., Gold L. Natural MS2 CP binding site binds weaker than the SELEX isolates. The experiment was performed using genomic SELEX. The invivo transcription of Ecoli genomic DNA was carried out to obtain the RNA. Subsequent purification of the interacting RNA was obained by reverse transcription and transcription to obtain the interacting RNA. 4 Nucleic Acids Res. (0305-1048) 2000 shtatland-2000-2 Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX. in vitro In vitro filter binding filter binding Filter overlay assay Filter overlay assay predetermined predetermined participant predetermined Shtatland T., Gill SC., Javornik BE., Johansson HE., Singer BS., Uhlenbeck OC., Zichi DA., Gold L. Natural MS2 CP binding site binds weaker than the SELEX isolates. The experiment was performed using genomic SELEX. The invivo transcription of Ecoli genomic DNA was carried out to obtain the RNA. Subsequent purification of the interacting RNA was obained by reverse transcription and transcription to obtain the interacting RNA. 4 Nucleic Acids Res. (0305-1048) 2000 0180 rna ribonucleic acid RNA rna ecolx Escherichia coli AAUGUUCCACCAGCAGGGGAAAUGAUGUUGUUCUGGCU This represents region 1001933 to 1001970 of the entry. This was an antisense transcript ygjl mrna messenger rna mRNA mrna ecolx Escherichia coli UAGGAGAGCGUUAACAACAGCAUCAGCGUUGAAGUGACGGAGGU This sequence represents region between bp 3224712 to 3224755 of the parent entry. mred mrna messenger rna mRNA mrna ecolx Escherichia coli UGAUUUGCAGCAACAGCGCAAUGAGGAAAGAGAGCCAGAUUACCC This sequence covers region between bp 3396825 and 3396869 of the entry. The RNA is a antisense transcript. secy mrna messenger rna mRNA mrna ecolx Escherichia coli UGACUGGACAUCAUCAGAGUUUGCACUUGAGC The sequence represents region between bp 3440837 to 3440868 of the entry. The sequence is an antisense transcript. phet mrna messenger rna mRNA mrna ecolx Escherichia coli CUUCGCUUCAGUACCGUCGAGCAGCACCAGCGUUUCGCC Region from 1795081 to 1795119 bp of parent entry. This was antisense transcript. capsd_bpms2 Capsid protein Coat protein protein protein bpms2 Enterobacteria phage MS2 MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY rffg mrna messenger rna mRNA mrna ecolx Escherichia coli GGCACGCGUAUUCACUGAGCAUCAGCCAGACUGUGU Region from 3970742 to 3970777 of entry is depicted. This was sense transcript. ebgr mrna messenger rna mRNA mrna ecolx Escherichia coli UAUUCUGGCUAUCUACAGCUACCAGCAGGAGCUGGAGAUCAACGAUCCU The sequence covers region between bp 3219679 to 3219727 of the entry and is a sense transcript. hyd rna ribonucleic acid RNA rna ecolx Escherichia coli UGAGUGCCGAAGAUCGUGAGCAGAGGAACACCCUGAUUAUCC mer94 rna ribonucleic acid RNA rna ecolx Escherichia coli AGUAAUUACGCCAUGAACACAGGCAUAAAGAAGUACAUAUGGU ms2cp-phet 297215 N/A 297217 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) physical association physical association false false false ms2cp-rffg 297215 N/A 297219 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) physical association physical association false false false ms2cp-0180 297215 N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) N/A 297220 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro physical association physical association false false false ms2cp-ygjl 297215 N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) N/A 297221 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro physical association physical association false false false ms2cp-mred 297215 N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) N/A 297222 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro physical association physical association false false false ms2cp-secy 297215 N/A 297223 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) physical association physical association false false false ms2cp-ebgr 297215 N/A 297224 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) physical association physical association false false false ms2cp-hyd 297215 N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) N/A 297225 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro physical association physical association false false false ms2cp-mer94 297215 N/A 297226 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) physical association physical association false false false ms2cp-rffg-1 297216 N/A 297219 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) physical association physical association false false false Disruption of consensus RNYA loop did not result in significant decrease in binding. ms2cp-ebgr-1 297216 N/A 297224 unspecified role unspecified role prey prey region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 297218 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) physical association physical association false false false