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/ peng-2020-1 in vitro In vitro 3d-em-single electron microscopy 3D single particle reconstruction 3D-EM-single experimental particp experimental participant identification experimental particp Peng W., Casey AK., Fernandez J., Carpinone EM., Servage KA., Chen Z., Li Y., Tomchick DR., Starai VJ., Orth K. Kim.Orth@UTSouthwestern.edu Nature structural & molecular biology 2020 imex curation Only protein-protein interactions imex curation peng-2020-2 in vitro In vitro pull down pull down experimental particp experimental participant identification experimental particp Peng W., Casey AK., Fernandez J., Carpinone EM., Servage KA., Chen Z., Li Y., Tomchick DR., Starai VJ., Orth K. Kim.Orth@UTSouthwestern.edu Nature structural & molecular biology 2020 imex curation Only protein-protein interactions imex curation peng-2020-3 yeast Saccharomyces cerevisiae Baker's yeast pull down pull down experimental particp experimental participant identification experimental particp Peng W., Casey AK., Fernandez J., Carpinone EM., Servage KA., Chen Z., Li Y., Tomchick DR., Starai VJ., Orth K. Kim.Orth@UTSouthwestern.edu Nature structural & molecular biology 2020 imex curation Only protein-protein interactions imex curation peng-2020-4 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column ms participant Identification by mass spectrometry ms participant Peng W., Casey AK., Fernandez J., Carpinone EM., Servage KA., Chen Z., Li Y., Tomchick DR., Starai VJ., Orth K. Kim.Orth@UTSouthwestern.edu Nature structural & molecular biology 2020 imex curation Only protein-protein interactions imex curation vatl1_yeast V-type proton ATPase subunit c VMA3 CLS7 CUP5 GEF2 YEL027W Vacuolar proton pump c subunit V-ATPase 16 kDa proteolipid subunit 1 Guanine nucleotide exchange factor 2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC FB8A142FFA1FA964 mint Proton-conducting pore forming subunit of the membrane integral V0 complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. It is an electrogenic proton pump that generates a proton motive force of 180 mv, inside positive and acidic, in the vacuolar membrane vesicles a0a4z7tvw3_vibph CGH73_02470 protein protein Vibrio parahaemolyticus Vibrio parahaemolyticus MVNTTQKISQSPVPDLEQFRAIAAQKDDRVISKRGEVKEPSTFHKGHKFASVSEGVLRKKYTKFFQENIKTHLDLKQALLKEEKPETALLAYSLVSPSGYRGEPLTERKILEVVSLLDEVKVDGDTYQQLKNTFDSISKDPRMQVSLENQYPGKMDGFGAQLLEMGKEKLKGSGVNAAINLALPGVGLLVATGRELHKASVNGDAEAYHHQLEQISQLPGRDQRLSMPMQQTLAIGHAMLSAEGAVGATLGMATGGLGTFGVSSVATAGVTPIAKEAIGTALATGIISGGGFVAGQAGAYGLNNEVQNQLKQGPMSGVLPRLEISNVKGDFTFSMQEPAAVRALMAYLGPKEDTSMSSPQAPKEAQEMEAARLTLKQMLGSSPNEHLVPDVDSLLKLSDEDMPSQTESTANGAFKKLLSEDWDWLMPAVRAMDKGEAGKINEKLTYKLPLDAANGRVYLDKSPNLSDAQLDALDKLGSPSQLRLMYLAEGWI The sequence has been withdrawn from uniprot. vatl2_yeast V-type proton ATPase subunit c' VMA11 CLS9 TFP3 YPL234C P1064 Vacuolar proton pump c' subunit V-ATPase 16 kDa proteolipid subunit 2 Proteolipid protein VMA11 Trifluoperazine resistance protein 3 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSLIPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVGDVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE C82D165064EEBBF7 vato_yeast V-type proton ATPase subunit c'' VMA16 PPA1 YHR026W Vacuolar proton pump c'' subunit V-ATPase 22 kDa proteolipid subunit protein protein yeast Saccharomyces cerevisiae Baker's yeast MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWANLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIVFSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSALFVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ 033FF5A516B97F8B yp17b_yeast Uncharacterized protein YPR170W-B YPR170W-B protein protein yeast Saccharomyces cerevisiae Baker's yeast MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAALVYLVFFVFCGFQVYLARRKPSIELR va0e_yeast V-type proton ATPase subunit e VMA9 CWH36 LDB10 Low dye-binding protein 10 Vacuolar proton pump subunit e YCL005W-A protein protein yeast Saccharomyces cerevisiae Baker's yeast MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLVAPRRSDLRPEFAE va0d_yeast V-type proton ATPase subunit d VMA6 YLR447C L9324.8 Vacuolar proton pump subunit d V-ATPase 39 kDa subunit V-ATPase subunit M39 protein protein yeast Saccharomyces cerevisiae Baker's yeast MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSSESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDKGEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEIIRNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSDLLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAFTQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY 53A19450CAF35632 voa1_yeast V0 assembly protein 1 YGR106C VOA1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDSAIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDELPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSLGWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVALSWISNLDITYGALEKSTNPIKKNN vph1_yeast V-type proton ATPase subunit a, vacuolar isoform VPH1 Vacuolar proton pump a subunit V-ATPase 95 kDa subunit Vacuolar pH protein 1 Vacuolar proton translocating ATPase subunit a 1 YOR270C protein protein yeast Saccharomyces cerevisiae Baker's yeast MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIRRLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEERLIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAIGASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFSHGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELYAIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARLGIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFAIMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYNDIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLSILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVKDGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTHKKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTIEFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFALTCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS 77709A914410CD4D a0a4z7tvw3_vibph-vma11-1 3973441 N/A 3973445 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973446 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated A0A4Z7TVW3:p.[Ala283Thr;Asn308Asp] [Thr304Ala; Asp329Asn] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false His Tag His Tag 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 in vitro In vitro Stoichiometry: 1.0 N/A 3973447 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973448 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973449 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973450 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973451 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973452 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973453 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated TAP tag TAP tag tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false in vitro In vitro Stoichiometry: 8.0 physical association physical association false false false Fig 1, Table 1, Fig 2 a0a4z7tvw3_vibph-vma11-2 3973441 N/A 3973445 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973446 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated His Tag His Tag 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 A0A4Z7TVW3:p.[Ala283Thr;Asn308Asp] [Thr304Ala; Asp329Asn] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false in vitro In vitro Stoichiometry: 1.0 N/A 3973447 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973448 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973449 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973450 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973451 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 1.0 N/A 3973452 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated in vitro In vitro Stoichiometry: 2.0 N/A 3973453 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component in vitro translated in vitro translated protein in vitro translated TAP tag TAP tag tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false in vitro In vitro Stoichiometry: 8.0 physical association physical association false false false Fig 1, Table 1 Two copies of VopQ molecule vph1-a0a4z7tvw3_vibph-2 3973442 N/A 3973446 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role prey prey over-expressed over expressed level over-expressed purified purified His Tag His Tag 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 A0A4Z7TVW3:p.Ser200Pro S200P mutation mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false A0A4Z7TVW3:p.[Asp204Ala;Glu206Ala] D204A/E206A mutation mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3973451 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3973453 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level purified purified TAP tag TAP tag tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeast Saccharomyces cerevisiae Baker's yeast association association false false false Edxt Data Fig 6c vph1-a0a4z7tvw3_vibph-1 3973442 N/A 3973446 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role prey prey over-expressed over expressed level over-expressed purified purified His Tag His Tag 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 155-316 region 155-316 region required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false 404-492 region 404-492 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) N/A 3973451 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3973453 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level purified purified TAP tag TAP tag tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeast Saccharomyces cerevisiae Baker's yeast association association false false false Extended Fig.6C vph1-vma6-1 3973443 N/A 3973451 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3973453 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level purified purified TAP tag TAP tag tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeast Saccharomyces cerevisiae Baker's yeast physical association physical association false false false Edxt Data Fig 6c a0a4z7tvw3_vibph-vma6-1 3973444 N/A 3973446 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified A0A4Z7TVW3:p.[Ala283Thr;Asn308Asp] [Thr304Ala; Asp329Asn] [304-304, 329-329] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false His Tag His Tag 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) Stoichiometry: 1.0 N/A 3973451 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 N/A 3973453 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 8.0 physical association physical association false false false Extended Data Fig 1