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/ plechanovov-2011-1 ecolx Escherichia coli solution sedimentati cosedimentation in solution solution sedimentati predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218694X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-2 in vitro In vitro comigration in sds comigration in sds page comigration in sds predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218707X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-3 in vitro In vitro comigration in sds comigration in sds page comigration in sds predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218699X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-4 ecolx Escherichia coli x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218695X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-5 in vitro In vitro pull down pull down predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218708X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-6 ecolx Escherichia coli molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218696X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-7 in vitro In vitro deubiquitinase assay deubiquitinase assay deubiquitinase assay predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218700X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-8 in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218704X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-9 in vitro In vitro ms of complexes mass spectrometry studies of complexes ms of complexes predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218701X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-10 in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218697X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-11 in vitro In vitro comigration in sds comigration in sds page comigration in sds predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218706X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-12 in vitro In vitro comigration in sds comigration in sds page comigration in sds predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218702X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-13 in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218705X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-14 in vitro In vitro fret fluorescent resonance energy transfer FRET RET FRET analysis FRET RET FRET analysis fret predetermined predetermined participant predetermined Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218703X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation plechanovov-2011-15 in vitro In vitro pull down pull down autoradiography autoradiography Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. DIP original experiment: DIP-218698X Nature structural & molecular biology 2011 IMEx Mechanism of ubiquitylation by dimeric RING ligase RNF4. Plechanovová A., Jaffray EG., McMahon SA., Johnson KA., Navrátilová I., Naismith JH., Hay RT. Only protein-protein interactions imex curation rnf4_rat E3 ubiquitin-protein ligase RNF4 RING finger protein 4 Small nuclear ring finger protein Snurf Rnf4 RING-type E3 ubiquitin transferase RNF4 protein protein rat Rattus norvegicus (Rat) Rat MSTRNPQRKRRGGAVNSRQTQKRTRETTSTPEISLEAEPIELVETVGDEIVDLTCESLEPVVVDLTHNDSVVIVEERRRPRRNGRRLRQDHADSCVVSSDDEELSKDKDVYVTTHTPRSTKDEGTTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI mint Enhances steroid receptor-mediated transcriptional activation as well as activating basal transcription ubiq_human UBIQ_HUMAN protein protein human Homo sapiens Human MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG sumo3_human Small ubiquitin-related modifier 3 SMT3 homolog 1 SUMO-2 SMT3H1 SUMO3 SMT3A Ubiquitin-like protein SMT3A protein protein human Homo sapiens Human MSEEKPKEGVKTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVPESSLAGHSF ubiq_bovin Ubiquitin RPS27A UBA80 UBCEP1 UBA52 UBCEP2 UBB UBC protein protein bovin Bos taurus (Bovine) Bovine MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG ub2d1_human Ubiquitin-conjugating enzyme E2 D1 Ubiquitin-protein ligase D1 Ubiquitin carrier protein D1 UbcH5 Ubiquitin-conjugating enzyme E2-17 kDa 1 Ubiquitin-conjugating enzyme E2(17)KB 1 UBC4/5 homolog Stimulator of Fe transport UBE2D1 UBCH5 UBCH5A SFT UBC5A (E3-independent) E2 ubiquitin-conjugating enzyme D1 E2 ubiquitin-conjugating enzyme D1 protein protein human Homo sapiens Human MALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM rnf4-1 3229479 N/A 3229494 unspecified role unspecified role unspecified role unspecified role RING domain Region 134-194 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 hub-sumo3-1 3229480 N/A 3229495 unspecified role unspecified role unspecified role unspecified role leu8ala L8A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ile44ala I44A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false val70ala V70A mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3229496 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false bub-ube2d1-1 3229481 N/A 3229497 unspecified role unspecified role unspecified role unspecified role bovin Bos taurus (Bovine) Bovine N/A 3229498 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false rnf4-3 3229482 N/A 3229494 unspecified role unspecified role unspecified role unspecified role RING domain Region 134-194 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 rnf4-hub-1 3229483 N/A 3229494 unspecified role unspecified role bait bait MBP-tag MBP-tag mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli N/A 3229495 unspecified role unspecified role prey prey ile44ala I44A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3229498 unspecified role unspecified role prey prey ecolx Escherichia coli physical association physical association false false false rnf4-4 3229484 N/A 3229494 unspecified role unspecified role unspecified role unspecified role p.Pro191_Ile194del Δ191-194 mutation disrupting mutation disrupting interaction mutation disrupting deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.Ile138Ala I138A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.His190Ala H190A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.Ile192Ala I192A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.Tyr193Ala Y193A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.Ile194Ala I194A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false rnf4-ube2d1-1 3229485 N/A 3229494 enzyme enzyme unspecified role unspecified role ecolx Escherichia coli N/A 3229498 enzyme target enzyme target substrate substrate unspecified role unspecified role ecolx Escherichia coli deubiquitination deubiquitination reaction deubiquitination false false false rnf4-bub-1 3229486 N/A 3229494 unspecified role unspecified role bait bait MBP-tag MBP-tag mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false RING domain Region 134-194 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.[Met140Ala;Arg181Ala] M140A/R181A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false O88846:p.Ile192Ala I192A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.Ile194Ala I194A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.Tyr193Ala Y193A/H mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.Tyr193His mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3229498 unspecified role unspecified role prey prey ecolx Escherichia coli N/A 3229497 unspecified role unspecified role prey prey bovin Bos taurus (Bovine) Bovine physical association physical association false false false bub-ube2d1-2 3229487 N/A 3229497 unspecified role unspecified role unspecified role unspecified role bovin Bos taurus (Bovine) Bovine N/A 3229498 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false rnf4-sumo3-1 3229488 N/A 3229494 unspecified role unspecified role bait bait Region 32-76 Region 32-76 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false MBP-tag MBP-tag mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false O88846:p.[Ile40Ala;Leu42Ala;Val43Ala;Ile50Ala;Val51Ala;Leu53Ala;Val61Ala;Val62Ala;Val63Ala;Val71Ala;Val72Ala;Ile73Ala;Val74Ala] I40A/L42A/V43A/I50A/V51A/L53A/V61A/V62A/V63A/V71A/V72A/I73A/V74A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3229496 unspecified role unspecified role prey prey ecolx Escherichia coli direct interaction direct interaction false false false hub-ube2d1-1 3229489 N/A 3229495 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3229498 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false bub-sumo3-1 3229490 N/A 3229497 unspecified role unspecified role unspecified role unspecified role bovin Bos taurus (Bovine) Bovine N/A 3229496 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false rnf4-ube2d1-2 3229491 N/A 3229494 unspecified role unspecified role bait bait MBP-tag MBP-tag mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli N/A 3229498 unspecified role unspecified role prey prey ecolx Escherichia coli physical association physical association false false false rnf4-5 3229492 N/A 3229494 unspecified role unspecified role fluorescence accept fluorescence acceptor fluorescence accept RING domain Region 134-194 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false YFP-tag YFP-tag yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false O88846:p.Ile194Ala I194A mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false O88846:p.[Met140Ala;Arg181Ala] M140A/R181A mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3229494 unspecified role unspecified role fluorescence donor fluorescence donor RING domain Region 134-194 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false CFP-tag CFP-tag cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli direct interaction direct interaction false false false sumo3-bub-1 3229493 N/A 3229497 unspecified role unspecified role prey prey 125I-label 125I-label 125i radiolabel 125i radiolabel I125 125I 125I I125 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false bovin Bos taurus (Bovine) Bovine N/A 3229496 unspecified role unspecified role bait bait 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 ecolx Escherichia coli physical association physical association false false false