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/ bleichert-2009-1 A dimeric structure for archaeal box C/D small ribonucleoproteins. in vitro In vitro density sedimentation cosedimentation through density gradient density sedimentation predetermined predetermined participant predetermined Bleichert F., Gagnon KT., Brown BA., Maxwell ES., Leschziner AE., Unger VM., Baserga SJ. Archaea - Interaction dataset based on Archaea proteins 10-25% glycerol gradient susan.baserga@yale.edu 2010-11-04: migleg@ibt.lt Science (0036-8075) 2009 Only protein-protein interactions imex curation bleichert-2009-2 A dimeric structure for archaeal box C/D small ribonucleoproteins. in vitro In vitro electron microscopy electron microscopy Electron crystallography Electron cryomicroscopy Electron crystallography Electron cryomicroscopy predetermined predetermined participant predetermined Bleichert F., Gagnon KT., Brown BA., Maxwell ES., Leschziner AE., Unger VM., Baserga SJ. Archaea - Interaction dataset based on Archaea proteins 10-25% glycerol gradient susan.baserga@yale.edu 2010-11-04: migleg@ibt.lt Science (0036-8075) 2009 Only protein-protein interactions imex curation rl7a_metja 50S ribosomal protein L7Ae rpl7ae Ribosomal protein L8e MJ1203 protein protein metja Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) Methanococcus jannaschii MAVYVKFKVPEEIQKELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEELKVLIEKVNVLKQ y694_metja Uncharacterized NOP5 family protein MJ0694 MJ0694 protein protein metja Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) Methanococcus jannaschii MIYVTFTPYGAFGVKDNKEVSGLEDIEYKKLFNEEEIPDIMFKLKTQPNKIADELKEEWGDEIKLETLSTEPFNIGEFLRNNLFKVGKELGYFNNYDEFRKKMHYWSTELTKKVIKSYAQQKDKIIIQVAEAISDLDKTLNLLSERLREWYSLYFPELDHLVNKHEVYANLITKLGKRKNFTKSQLKKILPSKLAGKIAEAAKNSMGGELEDYDLDVIVKFAEEINHLYEKRKELYNYLEKLMNEEAPNITKLAGVSLGARLIGLAGGLEKLAKMPASTIQVLGAEKALFAHLRMGVEPPKHGIIYNHPLIQGSPHWQRGKIARALACKLAIAARADYVGDYIADELLEKLNKRVEEIRRKYPKPPKKKKKEKPKAKKKEKKGKKEKSKKKKDKKKDKKGKKERKVIGKTKSRK flpa_metja Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase flpA MJ0697 protein protein metja Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) Methanococcus jannaschii MEDIKIKEIFENIYEVDLGDGLKRIATKSIVKGKKVYDEKIIKIGDEEYRIWNPNKSKLAAAIIKGLKVMPIKRDSKILYLGASAGTTPSHVADIADKGIVYAIEYAPRIMRELLDACAERENIIPILGDANKPQEYANIVEKVDVIYEDVAQPNQAEILIKNAKWFLKKGGYGMIAIKARSIDVTKDPKEIFKEQKEILEAGGFKIVDEVDIEPFEKDHVMFVGIWEGK sr8_metja_rna Methanocaldococcus jannaschii sR8 small RNA rna ribonucleic acid RNA rna methanocaldococcus jannaschii Methanocaldococcus jannaschii Methanococcus jannaschii flpa-rpl7ae-3 Assembly of the catalytically active box C/D sRNP complex 998141 n/a 998143 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) n/a 998144 unspecified role unspecified role neutral component neutral component region 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) n/a 998145 unspecified role unspecified role neutral component neutral component n-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) n/a 998146 unspecified role unspecified role neutral component neutral component physical association physical association false false false Figs. 1B, 1C Assembly required the presence of the sR8 small RNA rpl7ae-nop5-2 Assembly of the catalytically active box C/D sRNP complex 998141 n/a 998144 unspecified role unspecified role neutral component neutral component region 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) n/a 998143 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 3B rpl7ae-nop5-3 Assembly of the catalytically active box C/D sRNP complex 998141 n/a 998146 unspecified role unspecified role neutral component neutral component n/a 998144 unspecified role unspecified role neutral component neutral component region 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) n/a 998143 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 3A flpa-rpl7ae-4 Assembly of the catalytically active box C/D sRNP complex 998142 n/a 998145 unspecified role unspecified role neutral component neutral component n-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) n/a 998146 unspecified role unspecified role neutral component neutral component n/a 998144 unspecified role unspecified role neutral component neutral component region 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) n/a 998143 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 2A The EM structure was refined to a resolution of 27A rpl7ae-nop5-1 Assembly of the catalytically active box C/D sRNP complex 998142 n/a 998143 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) n/a 998146 unspecified role unspecified role neutral component neutral component n/a 998144 unspecified role unspecified role neutral component neutral component coiled coil region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 3A, 4A-C The Nop5 mutant lacking the coiled coil region still assembles into complexes containing all box C/D sRNP components, including the sRNA and L7, but they are not di-sRNPs i.e. are not catalytically active suggesting correct binding and assembly is impaired. rpl7ae-nop5-4 Assembly of the catalytically active box C/D sRNP complex 998142 n/a 998144 unspecified role unspecified role neutral component neutral component region 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) n/a 998143 unspecified role unspecified role neutral component neutral component n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 3B