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/ parent-2010-1 saltm Salmonella typhimurium tem transmission electron microscopy tem predetermined predetermined participant predetermined Parent KN., Khayat R., Tu LH., Suhanovsky MM., Cortines JR., Teschke CM., Johnson JE., Baker TS. DIP original experiment: DIP-216852X Structure (London, England : 1993) 2010 IMEx P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks. Parent KN., Khayat R., Tu LH., Suhanovsky MM., Cortines JR., Teschke CM., Johnson JE., Baker TS. Only protein-protein interactions imex curation olia-2011-1 ecolx Escherichia coli x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Olia AS., Prevelige PE., Johnson JE., Cingolani G. DIP original experiment: DIP-249029X Nature structural & molecular biology 2011 IMEx Three-dimensional structure of a viral genome-delivery portal vertex. Olia AS., Prevelige PE., Johnson JE., Cingolani G. Only protein-protein interactions imex curation olia-2011-2 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Olia AS., Prevelige PE., Johnson JE., Cingolani G. DIP original experiment: DIP-249030X Nature structural & molecular biology 2011 IMEx Three-dimensional structure of a viral genome-delivery portal vertex. Olia AS., Prevelige PE., Johnson JE., Cingolani G. Only protein-protein interactions imex curation roy-2012-1 ecolx Escherichia coli molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Roy A., Bhardwaj A., Datta P., Lander GC., Cingolani G. DIP original experiment: DIP-250503X Structure (London, England : 1993) 2012 IMEx Small terminase couples viral DNA binding to genome-packaging ATPase activity. Roy A., Bhardwaj A., Datta P., Lander GC., Cingolani G. Only protein-protein interactions imex curation roy-2012-2 ecolx Escherichia coli x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Roy A., Bhardwaj A., Datta P., Lander GC., Cingolani G. DIP original experiment: DIP-250500X Structure (London, England : 1993) 2012 IMEx Small terminase couples viral DNA binding to genome-packaging ATPase activity. Roy A., Bhardwaj A., Datta P., Lander GC., Cingolani G. Only protein-protein interactions imex curation roy-2012-3 ecolx Escherichia coli tem transmission electron microscopy tem predetermined predetermined participant predetermined Roy A., Bhardwaj A., Datta P., Lander GC., Cingolani G. DIP original experiment: DIP-250501X Structure (London, England : 1993) 2012 IMEx Small terminase couples viral DNA binding to genome-packaging ATPase activity. Roy A., Bhardwaj A., Datta P., Lander GC., Cingolani G. Only protein-protein interactions imex curation roy-2012-4 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column weight by staining molecular weight estimation by staining weight by staining Roy A., Bhardwaj A., Datta P., Lander GC., Cingolani G. DIP original experiment: DIP-250502X Structure (London, England : 1993) 2012 IMEx Small terminase couples viral DNA binding to genome-packaging ATPase activity. Roy A., Bhardwaj A., Datta P., Lander GC., Cingolani G. Only protein-protein interactions imex curation olia-2007-1 ecolx Escherichia coli x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Olia AS., Casjens S., Cingolani G. DIP original experiment: DIP-254830X Nature structural & molecular biology 2007 IMEx Structure of phage P22 cell envelope–penetrating needle. Olia AS., Casjens S., Cingolani G. Only protein-protein interactions imex curation tang-2006-13 in vitro In vitro 3d-em 3D electron microscopy 3D-EM electron tomog predetermined predetermined participant predetermined Tang L., Gilcrease EB., Casjens SR., Johnson JE. DIP original experiment: DIP-66311X Structure (London, England : 1993) 2006 IMEx Highly discriminatory binding of capsid-cementing proteins in bacteriophage L. Tang L., Gilcrease EB., Casjens SR., Johnson JE. Only protein-protein interactions imex curation tang-2006-14 ecolx Escherichia coli 3d-em 3D electron microscopy 3D-EM electron tomog predetermined predetermined participant predetermined Tang L., Gilcrease EB., Casjens SR., Johnson JE. DIP original experiment: DIP-66310X Structure (London, England : 1993) 2006 IMEx Highly discriminatory binding of capsid-cementing proteins in bacteriophage L. Tang L., Gilcrease EB., Casjens SR., Johnson JE. Only protein-protein interactions imex curation capsd_bpp22 Major capsid protein 5 Gene product 5 Major head protein protein protein bpp22 Salmonella phage P22 Bacteriophage P22 MALNEGQIVTLAVDEIIETISAITPMAQKAKKYTPPAASMQRSSNTIWMPVEQESPTQEGWDLTDKATGLLELNVAVNMGEPDNDFFQLRADDLRDETAYRRRIQSAARKLANNVELKVANMAAEMGSLVITSPDAIGTNTADAWNFVADAEEIMFSRELNRDMGTSYFFNPQDYKKAGYDLTKRDIFGRIPEEAYRDGTIQRQVAGFDDVLRSPKLPVLTKSTATGITVSGAQSFKPVAWQLDNDGNKVNVDNRFATVTLSATTGMKRGDKISFAGVKFLGQMAKNVLAQDATFSVVRVVDGTHVEITPKPVALDDVSLSPEQRAYANVNTSLADAMAVNILNVKDARTNVFWADDAIRIVSQPIPANHELFAGMKTTSFSIPDVGLNGIFATQGDISTLSGLCRIALWYGVNATRPEAIGVGLPGQTA needl_bpp22 Tail needle protein gp26 26 Head completion protein Packaged DNA stabilization protein Tail accessory factor gp26 protein protein bpp22 Salmonella phage P22 Bacteriophage P22 MADPSLNNPVVIQATRLDASILPRNVFSKSYLLYVIAQGTDVGAIAGKANEAGQGAYDAQVKNDEQDVELADHEARIKQLRIDVDDHESRITANTKAITALNVRVTTAEGEIASLQTNVSALDGRVTTAENNISALQADYVSKTATTSQSLASPLNVTTSYSVGGKKVLGARQTGWTAATGTANKGVFDADLTFAVSDTYTQSEIQAIANALITERRRTKALEDALRAHGLID exlys_bpp22 Peptidoglycan hydrolase gp4 4 Gene product 4 Internal virion protein gp4 Tail adapter protein gp4 protein protein bpp22 Salmonella phage P22 Bacteriophage P22 MQIKTKGDLVRAALRKLGVASDATLTDVEPQSMQDAVDDLEAMMAEWYQDGKGIITGYVFSDDENPPAEGDDHGLRSSAVSAVFHNLACRIAPDYALEATAKIIATAKYGKELLYKQTAISRAKRAPYPSRMPTGSGNSFANLNEWHYFPGEQNADSTTPHDEGNG portl_bpp22 Portal protein 1 Gene product 1 Head-to-tail connector protein protein bpp22 Salmonella phage P22 Bacteriophage P22 MADNENRLESILSRFDADWTASDEARREAKNDLFFSRVSQWDDWLSQYTTLQYRGQFDVVRPVVRKLVSEMRQNPIDVLYRPKDGARPDAADVLMGMYRTDMRHNTAKIAVNIAVREQIEAGVGAWRLVTDYEDQSPTSNNQVIRREPIHSACSHVIWDSNSKLMDKSDARHCTVIHSMSQNGWEDFAEKYDLDADDIPSFQNPNDWVFPWLTQDTIQIAEFYEVVEKKETAFIYQDPVTGEPVSYFKRDIKDVIDDLADSGFIKIAERQIKRRRVYKSIITCTAVLKDKQLIAGEHIPIVPVFGEWGFVEDKEVYEGVVRLTKDGQRLRNMIMSFNADIVARTPKKKPFFWPEQIAGFEHMYDGNDDYPYYLLNRTDENSGDLPTQPLAYYENPEVPQANAYMLEAATSAVKEVATLGVDTEAVNGGQVAFDTVNQLNMRADLETYVFQDNLATAMRRDGEIYQSIVNDIYDVPRNVTITLEDGSEKDVQLMAEVVDLATGEKQVLNDIRGRYECYTDVGPSFQSMKQQNRAEILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPETPEEQQWLVEAQQAKQGQQDPAMVQAQGVLLQGQAELAKAQNQTLSLQIDAAKVEAQNQLNAARIAEIFNNMDLSKQSEFREFLKTVASFQQDRSEDARANAELLLKGDEQTHKQRMDIANILQSQRQNQPSGSVAETPQ ters_bpp22 Terminase, small subunit 3 DNA-packaging protein gp3 protein protein bpp22 Salmonella phage P22 Bacteriophage P22 MAAPKGNRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPDKGDRDKRRSRIKELFNRGTGRDS terl_bpp22 Terminase, large subunit 2 DNA-packaging protein gp2 protein protein bpp22 Salmonella phage P22 Bacteriophage P22 MELDAILDNLSDEEQIELLELLEEEENYRNTHLLYEFAPYSKQREFIDAGHDYPERCFMAGNQLGKSFTGAAEVAFHLTGRYPGTKGYPADGKYGGEWKGKRFYEPVVFWIGGETNETVTKTTQRILCGRIEENDEPGYGSIPKEDIISWKKSPFFPNLVDHLLVKHHTADGVEDGISICYFKPYSQGRARWQGDTIHGVWFDEEPPYSIYGEGLTRTNKYGQFSILTFTPLMGMSDVVTKFLKNPSKSQKVVNMTIYDAEHYTDEQKEQIIASYPEHEREARARGIPTMGSGRIFQIPEETIKCQPFECPDHFYVIDAQDFGWNHPQAHIQLWWDKDADVFYLARVWKKSENTAVQAWGAVKSWANKIPVAWPHDGHQHEKGGGEQLKTQYADAGFSMLPDHATFPDGGNSVESGISELRDLMLEGRFKVFNTCEPFFEEFRLYHRDENGKIVKTNDDVLDATRYGYMMRRFARMMRDIRKPKEKKIPAPIRPVRRGR q5c838_9caud dec protein protein Enterobacteria phage L Enterobacteria phage L MANPNFTPSWPLYKDADGVYVSALPIKAIKYANDGSANAEFDGPYADQYMSAQTVAVFKPEVGGYLFRSQYGELLYMSKTAFEANYTSASGSVANAETADKLSTARTITLTGAVTGSASFDGSANVTIETTSGS 5-8 3205976 N/A 3205977 unspecified role unspecified role unspecified role unspecified role saltm Salmonella typhimurium direct interaction direct interaction false false false 1-121 3225228 N/A 3225230 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false 1-122 3225229 N/A 3225231 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3225230 unspecified role unspecified role unspecified role unspecified role Core domain Region 1-602 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false 3-1 3242263 N/A 3242267 unspecified role unspecified role unspecified role unspecified role Region 1-139 Region 1-139 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false 3-2 3242264 N/A 3242267 unspecified role unspecified role unspecified role unspecified role Region 1-139 Region 1-139 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false 3-3 3242265 N/A 3242267 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false 2-3 3242266 N/A 3242268 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3242267 unspecified role unspecified role unspecified role unspecified role Region 140-162 Region 140-162 required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false 26-1 3165005 N/A 3165006 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false 5-dec-1 3144081 N/A 3205977 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3144083 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false 5-1 3144082 N/A 3205977 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/ bonvin-1994-1 in vitro In vitro nmr nuclear magnetic resonance NMR NMR nmr predetermined predetermined participant predetermined Bonvin AM., Vis H., Breg JN., Burgering MJ., Boelens R., Kaptein R. Journal of molecular biology 1994 Only protein-protein interactions imex curation imex curation rarc_bpp22 Transcriptional repressor arc arc protein protein bpp22 Salmonella phage P22 Bacteriophage P22 MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA arc-arc-1 3712536 N/A 3712537 unspecified role unspecified role neutral component neutral component purified purified arc repressor sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 3712537 unspecified role unspecified role neutral component neutral component purified purified arc repressor sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 3712542 3712540 direct interaction direct interaction false false false Fig 3