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/ zhang-2020-14 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Zhang L., Liu MR., Yao YC., Bostrom IK., Wang YD., Chen AQ., Li JX., Gu SH., Ji CN. chnji@fudan.edu.cn Acta crystallographica. Section F, Structural biology communications 2020 Only protein-protein interactions imex curation imex curation zhang-2020-15 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 Zhang L., Liu MR., Yao YC., Bostrom IK., Wang YD., Chen AQ., Li JX., Gu SH., Ji CN. chnji@fudan.edu.cn Acta crystallographica. Section F, Structural biology communications 2020 Only protein-protein interactions imex curation imex curation efremov-2011-1 ecobd Escherichia coli (strain B / BL21-DE3) x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Efremov RG., Sazanov LA. DIP original experiment: DIP-218973X Nature 2011 IMEx Structure of the membrane domain of respiratory complex I. Efremov RG., Sazanov LA. Only protein-protein interactions imex curation efremov-2011-2 ecobd Escherichia coli (strain B / BL21-DE3) ion exchange chrom ion exchange chromatography IEC IEC ion exchange chrom predetermined predetermined participant predetermined Efremov RG., Sazanov LA. DIP original experiment: DIP-218974X Nature 2011 IMEx Structure of the membrane domain of respiratory complex I. Efremov RG., Sazanov LA. Only protein-protein interactions imex curation a0a140n7p6_ecobd ECBD_1383 protein protein ecobd Escherichia coli (strain B / BL21-DE3) MNMLALTIILPLIGFVLLAFSRGRWSENVSAIVGVGSVGLAALVTAFIGVDFFANGEQTYSQPLWTWMSVGDFNIGFNLVLDGLSLTMLSVVTGVGFLIHMYASWYMRGEEGYSRFFAYTNLFIASMVVLVLADNLLLMYLGWEGVGLCSYLLIGFYYTDPKNGAAAMKAFVVTRVGDVFLAFALFILYNELGTLNFREMVELAPAHFADGNNMLMWATLMLLGGAVGKSAQLPLQTWLADAMAGPTPVSALIHAATMVTAGVYLIARTHGLFLMTPEVLHLVGIVGAVTLLLAGFAALVQTDIKRVLAYSTMSQIGYMFLALGVQAWDAAIFHLMTHAFFKALLFLASGSVILACHHEQNIFKMGGLRKSIPLVYLCFLVGGAALSALPLVTAGFFSKDEILAGAMANGHINLMVAGLVGAFMTSLYTFRMIFIVFHGKEQIHAHAVKGVTHSLPLIVLLILSTFVGALIVPPLQGVLPQTTELAHGSMLTLEITSGVVAVVGILLAAWLWLGKRTLVTSIANSAPGRLLSTWWYNAWGFDWLYDKVFVKPFLGIAWLLKRDPLNSMMNIPAVLSRFAGKGLLLSENGYLRWYVASMSIGAVVVLALLMVLR a0a140n7n4_ecobd NADH-quinone oxidoreductase subunit A nuoA NADH dehydrogenase I subunit A NDH-1 subunit A NUO1 ECBD_1373 protein protein ecobd Escherichia coli (strain B / BL21-DE3) MSMSTSTEVIAHHWAFAIFLIVAIGLCCLMLVGGWFLGGRARARSKNVPFESGIDSVGSARLRLSAKFYLVAMFFVIFDVEALYLFAWSTSIRESGWVGFVEAAIFIFVLLAGLVYLVRIGALDWTPARSRRERMNPETNSIANRQR a0a140n755_ecobd NADH-quinone oxidoreductase subunit N nuoN NADH dehydrogenase I subunit N NDH-1 subunit N ECBD_1385 protein protein ecobd Escherichia coli (strain B / BL21-DE3) MTITPQNLIALLPLLIVGLTVVVVMLSIAWRRNHFLNATLSVIGLNAALVSLWFVGQAGAMDVTPLMRVDGFAMLYTGLVLLASLATCTFAYPWLEGYNDNKDEFYLLVLIAALGGILLANANHLASLFLGIELISLPLFGLVGYAFRQKRSLEASIKYTILSAAASSFLLFGMALVYAQSGDLSFVALGKNLGDGMLNEPLLLAGFGLMIVGLGFKLSLVPFHLWTPDVYQGAPAPVSTFLATASKIAIFGVVMRLFLYAPVGDSEAIRVVLAIIAFASIIFGNLMALSQTNIKRLLGYSSISHLGYLLVALIALQTGEMSMEAVGVYLAGYLFSSLGAFGVVSLMSSPYRGPDADSLFSYRGLFWHRPILAAVMTVMMLSLAGIPMTLGFIGKFYVLAVGVQAHLWWLVGAVVVGSAIGLYYYLRVAVSLYLHAPEQPGRDAPSNWQYSAGGIVVLISALLVLVLGVWPQPLISIVRLAMPLM a0a140n571_ecobd NADH dehydrogenase I subunit M NADH-quinone oxidoreductase subunit M NDH-1 subunit M ECBD_1384 protein protein ecobd Escherichia coli (strain B / BL21-DE3) MLLPWLILIPFIGGFLCWQTERFGVKVPRWIALITMGLTLALSLQLWLQGGYSLTQSAGIPQWQSEFDMPWIPRFGISIHLAIDGLSLLMVVLTGLLGVLAVLCSWKEIEKYQGFFHLNLMWILGGVIGVFLAIDMFLFFFFWEMMLVPMYFLIALWGHKASDGKTRITAATKFFIYTQASGLVMLIAILALVFVHYNATGVWTFNYEELLNTPMSSGVEYLLMLGFFIAFAVKMPVVPLHGWLPDAHSQAPTAGSVDLAGILLKTAAYGLLRFSLPLFPNASAEFAPIAMWLGVIGIFYGAWMAFAQTDIKRLIAYTSVSHMGFVLIAIYTGSQLAYQGAVIQMIAHGLSAAGLFILCGQLYERIHTRDMRMMGGLWSKMKWLPALSLFFAVATLGMPGTGNFVGEFMILFGSFQVVPVITVISTFGLVFASVYSLAMLHRAYFGKAKSQIASQELPGMSLRELFMILLLVVLLVLLGFYPQPILDTSHSAIGNIQQWFVNSVTTTRP nuok_ecobd NADH-quinone oxidoreductase subunit K nuoK NADH dehydrogenase I subunit K NDH-1 subunit K B21_02164 ECBD_1382 ECD_02204 protein protein ecobd Escherichia coli (strain B / BL21-DE3) MIPLQHGLILAAILFVLGLTGLVIRRNLLFMLIGLEIMINASALAFVVAGSYWGQTDGQVMYILAISLAAAEASIGLALLLQLHRRRQNLNIDSVSEMRG a0a140n7w8_ecobd NADH-quinone oxidoreductase subunit J ECBD_1381 protein protein ecobd Escherichia coli (strain B / BL21-DE3) MEFAFYICGLIAILATLRVITHTNPVHALLYLIISLLAISGVFFSLGAYFAGALEIIVYAGAIMVLFVFVVMMLNLGGSEIEQERQWLKPQVWIGPAILSAIMLVVIVYAILGVNDQGIDGTPISAKAVGITLFGPYVLAVELASMLLLAGLVVAFHVGREERAGEVLSNRKDDSAKRKTEEHA a0a140nck4_ecobd Glyceraldehyde-3-phosphate dehydrogenase ECBD_2224 protein protein ecobd Escherichia coli (strain B / BL21-DE3) MSKVGINGFGRIGRLVLRRLLEVKSNIDVVAINDLTSPKILAYLLKHDSNYGPFPWSVDFTEDSLIVDGKSIAVYAEKEAKNIPWKAKGAEIIVECTGFYTSAEKSQAHLDAGAKKVLISAPAGEMKTIVYNVNDDTLDGNDTIVSVASCTTNCLAPMAKALHDSFGIEVGTMTTIHAYTGTQSLVDGPRGKDLRASRAAAENIIPHTTGAAKAIGLVIPELSGKLKGHAQRVPVKTGSVTELVSILGKKVTAEEVNNALKQATTNNESFGYTDEEIVSSDIIGSHFGSVFDATQTEITAVGDLQLVKTVAWYDNEYGFVTQLIRTLEKFAKL a0a140nck4_ecobd-1 4110080 N/A 4110082 unspecified role unspecified role neutral component neutral component purified purified binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 physical association physical association false false false Fig 3, Table 2-3 a0a140nck4_ecobd-2 4110081 N/A 4110082 unspecified role unspecified role neutral component neutral component purified purified binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 physical association physical association false false false Fig 1 nuoa-nuoj-3 3294444 N/A 3294446 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294447 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294448 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294449 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294450 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294451 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) physical association physical association false false false nuoa-nuoj-4 3294445 N/A 3294446 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294447 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294448 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294449 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294450 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) N/A 3294451 unspecified role unspecified role unspecified role unspecified role ecobd Escherichia coli (strain B / BL21-DE3) association association false false false MINT MINT, Dpt of Biology, University of Rome Tor Vergata MINT http://mint.bio.uniroma2.it/mint url>http://mint.bio.uniroma2.it/mint/ https://mint.bio.uniroma2.it MINT-[0-9]+ https://mint.bio.uniroma2.it/index.php/results-interactions/?id=${ac} The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it http://mint.bio.uniroma2.it/mint ahn-2015-2 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Ahn JW., Chang JH., Kim KJ. jhcbio@knu.ac.kr, kkim@knu.ac.kr FEBS letters 2015 Only protein-protein interactions imex curation imex curation ahn-2015-3 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Ahn JW., Chang JH., Kim KJ. jhcbio@knu.ac.kr, kkim@knu.ac.kr FEBS letters 2015 Only protein-protein interactions imex curation imex curation ygea_ecobd L-aspartate/glutamate-specific racemase ygeA EcL-DER ECBD_0884 protein protein ecobd Escherichia coli (strain B / BL21-DE3) MKTIGLLGGMSWESTIPYYRLINEGIKQRLGGLHSAQVLLHSVDFHEIEECQRRGEWDKTGDILAEAALGLQRAGAEGIVLCTNTMHKVADAIESRCTLPFLHIADATGRAITGAGMTRVALLGTRYTMEQDFYRGRLTEQFSINCLIPEADERAKINQIIFEELCLGQFTEASRAYYAQVIARLAEQGAQGVIFGCTEIGLLVPEERSVLPVFDTAAIHAEDAVAFMLS c6ej28_ecobd-2 1894429 n/a 1894431 unspecified role unspecified role neutral component neutral component purified purified direct interaction direct interaction false false false t1 f1b In order to elucidate the function and substrate specificity of the gene product of B21_02649 from E. coli, we determined a crystal structure of B21_02649 at a resolution of 1.8 Å. The crystal belonged to C2221, and an asymmetric unit of structure contains two molecules (Fig. 1A and B). This suggests that the protein functions as a dimer, which is consistent with size-exclusion chromatography results (Fig. 1C) c6ej28_ecobd-1 1894430 n/a 1894431 unspecified role unspecified role neutral component neutral component purified purified direct interaction direct interaction false false false f1c In order to elucidate the function and substrate specificity of the gene product of B21_02649 from E. coli, we determined a crystal structure of B21_02649 at a resolution of 1.8 Å. The crystal belonged to C2221, and an asymmetric unit of structure contains two molecules (Fig. 1A and B). This suggests that the protein functions as a dimer, which is consistent with size-exclusion chromatography results (Fig. 1C)