#ID(s) interactor A	ID(s) interactor B	Alt. ID(s) interactor A	Alt. ID(s) interactor B	Alias(es) interactor A	Alias(es) interactor B	Interaction detection method(s)	Publication 1st author(s)	Publication Identifier(s)	Taxid interactor A	Taxid interactor B	Interaction type(s)	Source database(s)	Interaction identifier(s)	Confidence value(s)	Expansion method(s)	Biological role(s) interactor A	Biological role(s) interactor B	Experimental role(s) interactor A	Experimental role(s) interactor B	Type(s) interactor A	Type(s) interactor B	Xref(s) interactor A	Xref(s) interactor B	Interaction Xref(s)	Annotation(s) interactor A	Annotation(s) interactor B	Interaction annotation(s)	Host organism(s)	Interaction parameter(s)	Creation date	Update date	Checksum(s) interactor A	Checksum(s) interactor B	Interaction Checksum(s)	Negative	Feature(s) interactor A	Feature(s) interactor B	Stoichiometry(s) interactor A	Stoichiometry(s) interactor B	Identification method participant A	Identification method participant B
uniprotkb:P25694	uniprotkb:P33755	intact:EBI-4308|ensemblfungi:YDL126C|uniprotkb:D6VRM4	intact:EBI-12193|uniprotkb:D6VQG6|ensemblfungi:YBR170C	psi-mi:cdc48_yeast(display_long)|uniprotkb:CDC48(gene name)|psi-mi:CDC48(display_short)|uniprotkb:Cell division cycle protein 48(gene name synonym)|uniprotkb:Transitional endoplasmic reticulum ATPase homolog(gene name synonym)|uniprotkb:YDL126C(locus name)	psi-mi:npl4_yeast(display_long)|uniprotkb:NPL4(gene name)|psi-mi:NPL4(display_short)|uniprotkb:YBR170C(locus name)|uniprotkb:YBR1231(orf name)|uniprotkb:HRD4(gene name synonym)|uniprotkb:HMG-CoA reductase degradation protein 4(gene name synonym)	psi-mi:"MI:0410"(3D electron microscopy)	Twomey et al. (2019)	pubmed:31249135|imex:IM-27726	taxid:559292(yeast)|taxid:559292(Saccharomyces cerevisiae)	taxid:559292(yeast)|taxid:559292(Saccharomyces cerevisiae)	psi-mi:"MI:0915"(physical association)	psi-mi:"MI:0465"(DIP)	intact:EBI-21915206|imex:IM-27726-1|emdb:EMD-0665|emdb:EMD-0666|emdb:EMD-20000	-	psi-mi:"MI:1060"(spoke expansion)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0497"(neutral component)	psi-mi:"MI:0497"(neutral component)	psi-mi:"MI:0326"(protein)	psi-mi:"MI:0326"(protein)	refseq:NP_010157.1|sgd:S000002284|ensemblfungi:YDL126C(gene)|ensemblfungi:YDL126C_mRNA(transcript)|go:"GO:0000837"(Doa10p ubiquitin ligase complex)|dip:DIP-2704N|mint:P25694|go:"GO:0000839"(Hrd1p ubiquitin ligase ERAD-L complex)|go:"GO:0005524"(ATP binding)|go:"GO:0005634"(nucleus)|go:"GO:0005739"(mitochondrion)|go:"GO:0005789"(endoplasmic reticulum membrane)|go:"GO:0005829"(cytosol)|go:"GO:0006274"(DNA replication termination)|go:"GO:0010636"(positive regulation of mitochondrial fusion)|go:"GO:0016236"(macroautophagy)|go:"GO:0016320"(endoplasmic reticulum membrane fusion)|go:"GO:0016887"(ATP hydrolysis activity)|go:"GO:0019888"(protein phosphatase regulator activity)|go:"GO:0030433"(ubiquitin-dependent ERAD pathway)|go:"GO:0030894"(replisome)|go:"GO:0030970"(retrograde protein transport, ER to cytosol)|go:"GO:0031134"(sister chromatid biorientation)|go:"GO:0031593"(polyubiquitin modification-dependent protein binding)|go:"GO:0034098"(VCP-NPL4-UFD1 AAA ATPase complex)|go:"GO:0034517"(ribophagy)|go:"GO:0034727"(piecemeal microautophagy of the nucleus)|go:"GO:0036266"(Cdc48p-Npl4p-Vms1p AAA ATPase complex)|go:"GO:0042802"(identical protein binding)|go:"GO:0043130"(ubiquitin binding)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0043328"(protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway)|go:"GO:0043332"(mating projection tip)|go:"GO:0043624"|go:"GO:0046034"(ATP metabolic process)|go:"GO:0051228"(mitotic spindle disassembly)|go:"GO:0051974"(negative regulation of telomerase activity)|go:"GO:0070651"(nonfunctional rRNA decay)|go:"GO:0071629"(cytoplasm protein quality control by the ubiquitin-proteasome system)|go:"GO:0071630"(nuclear protein quality control by the ubiquitin-proteasome system)|go:"GO:0071712"(ER-associated misfolded protein catabolic process)|go:"GO:0072671"(mitochondria-associated ubiquitin-dependent protein catabolic process)|go:"GO:0097352"(autophagosome maturation)|go:"GO:0120174"(stress-induced homeostatically regulated protein degradation pathway)|go:"GO:0140603"(obsolete ATP hydrolysis activity)|go:"GO:1900182"(positive regulation of protein localization to nucleus)|go:"GO:1990112"(RQC complex)|go:"GO:1990116"(ribosome-associated ubiquitin-dependent protein catabolic process)|go:"GO:1990171"(SCF complex disassembly in response to cadmium stress)|go:"GO:2001168"(positive regulation of histone H2B ubiquitination)|interpro:IPR003338(AAA ATPase VAT, N-terminal)|interpro:IPR003593(AAA+ ATPase, core)|interpro:IPR003959(AAA ATPase, core)|interpro:IPR003960(AAA ATPase, conserved site)|interpro:IPR004201(Cell division protein 48, CDC48, domain 2)|interpro:IPR005938(AAA ATPase, CDC48)|interpro:IPR009010(Aspartate decarboxylase-like fold)|interpro:IPR015415(Vps4 oligomerisation, C-terminal)|interpro:IPR027417|interpro:IPR029067|interpro:IPR041569|rcsb pdb:6OA9|rcsb pdb:6OAA|rcsb pdb:6OAB|rcsb pdb:6OMB|rcsb pdb:6OPC|reactome:R-SCE-110320|reactome:R-SCE-3371511|reactome:R-SCE-532668|reactome:R-SCE-5358346|reactome:R-SCE-5689896|reactome:R-SCE-6798695|reactome:R-SCE-8876725	ensemblfungi:YBR170C(gene)|ensemblfungi:YBR170C_mRNA(transcript)|go:"GO:0000837"(Doa10p ubiquitin ligase complex)|go:"GO:0000839"(Hrd1p ubiquitin ligase ERAD-L complex)|go:"GO:0005634"(nucleus)|go:"GO:0005737"(cytoplasm)|go:"GO:0006274"(DNA replication termination)|go:"GO:0006511"(ubiquitin-dependent protein catabolic process)|go:"GO:0030433"(ubiquitin-dependent ERAD pathway)|go:"GO:0030894"(replisome)|go:"GO:0030970"(retrograde protein transport, ER to cytosol)|go:"GO:0031625"(ubiquitin protein ligase binding)|go:"GO:0031965"(nuclear membrane)|go:"GO:0034098"(VCP-NPL4-UFD1 AAA ATPase complex)|go:"GO:0036266"(Cdc48p-Npl4p-Vms1p AAA ATPase complex)|go:"GO:0042175"(nuclear outer membrane-endoplasmic reticulum membrane network)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0051028"(mRNA transport)|go:"GO:0051228"(mitotic spindle disassembly)|go:"GO:0051974"(negative regulation of telomerase activity)|go:"GO:0070651"(nonfunctional rRNA decay)|go:"GO:0071629"(cytoplasm protein quality control by the ubiquitin-proteasome system)|go:"GO:0071712"(ER-associated misfolded protein catabolic process)|go:"GO:0072665"(protein localization to vacuole)|go:"GO:0072671"(mitochondria-associated ubiquitin-dependent protein catabolic process)|go:"GO:1900182"(positive regulation of protein localization to nucleus)|go:"GO:1990112"(RQC complex)|go:"GO:1990116"(ribosome-associated ubiquitin-dependent protein catabolic process)|interpro:IPR007716(NPL4, zinc-binding putative)|go:"GO:0043130"(ubiquitin binding)|interpro:IPR016563(Polyubiquitin-tagged protein recognition complex, Npl4 component)|interpro:IPR029071|interpro:IPR037518|rcsb pdb:6JWH|rcsb pdb:6JWI|rcsb pdb:6JWJ|interpro:IPR007717(NPL4)|rcsb pdb:6OA9|rcsb pdb:6OAA|reactome:R-SCE-110320|refseq:NP_009729.1|sgd:S000000374|dip:DIP-1475N|mint:P33755	wwpdb:6OA9(subset)|wwpdb:6OAA(subset)|wwpdb:6OAB(subset)	crc64:02ADDB9A227614D8	crc64:6EF35D21338EE07E	figure legend:Fig 1, Table S1|full coverage:Only protein-protein interactions|curation depth:imex curation	taxid:-1(in vitro)|taxid:-1(In vitro)	-	2019/07/13	2020/06/23	rogid:qM/04kWcyjkQ3QCa3WklyvhNigE559292	rogid:2+0sYJtYCsEX5lm8Tk91hNDj8II559292	rigid:wX0IdG8fuVmAlLsUI4m14/3+b8Y	false	mutation:588-588	-	6	1	psi-mi:"MI:2287"(identification by structure determination)	psi-mi:"MI:2287"(identification by structure determination)
uniprotkb:P25694	intact:EBI-19797	intact:EBI-4308|ensemblfungi:YDL126C|uniprotkb:D6VRM4	dip:DIP-1549N|uniprotkb:P04838|uniprotkb:Q6LA96	psi-mi:cdc48_yeast(display_long)|uniprotkb:CDC48(gene name)|psi-mi:CDC48(display_short)|uniprotkb:Cell division cycle protein 48(gene name synonym)|uniprotkb:Transitional endoplasmic reticulum ATPase homolog(gene name synonym)|uniprotkb:YDL126C(locus name)	psi-mi:ubiq_yeast(display_short)|psi-mi:EBI-19797(display_long)|uniprotkb:UBI1(gene name)|psi-mi:UBI1(display_short)|uniprotkb:RPL40A(gene name synonym)|uniprotkb:YIL148W(locus name)|uniprotkb:UBI2(gene name)|psi-mi:UBI2(display_short)|uniprotkb:RPL40B(gene name synonym)|uniprotkb:YKR094C(locus name)|uniprotkb:UBI3(gene name)|psi-mi:UBI3(display_short)|uniprotkb:RPS31(gene name synonym)|uniprotkb:YLR167W(locus name)|uniprotkb:L9470.14(orf name)|uniprotkb:UBI4(gene name)|psi-mi:UBI4(display_short)|uniprotkb:SCD2(gene name synonym)|uniprotkb:YLL039C(locus name)	psi-mi:"MI:0410"(3D electron microscopy)	Twomey et al. (2019)	pubmed:31249135|imex:IM-27726	taxid:559292(yeast)|taxid:559292(Saccharomyces cerevisiae)	taxid:4932(yeasx)|taxid:4932("Saccharomyces cerevisiae (Baker's yeast)")	psi-mi:"MI:0915"(physical association)	psi-mi:"MI:0465"(DIP)	intact:EBI-21915206|imex:IM-27726-1|emdb:EMD-0665|emdb:EMD-0666|emdb:EMD-20000	-	psi-mi:"MI:1060"(spoke expansion)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0497"(neutral component)	psi-mi:"MI:0497"(neutral component)	psi-mi:"MI:0326"(protein)	psi-mi:"MI:0326"(protein)	refseq:NP_010157.1|sgd:S000002284|ensemblfungi:YDL126C(gene)|ensemblfungi:YDL126C_mRNA(transcript)|go:"GO:0000837"(Doa10p ubiquitin ligase complex)|dip:DIP-2704N|mint:P25694|go:"GO:0000839"(Hrd1p ubiquitin ligase ERAD-L complex)|go:"GO:0005524"(ATP binding)|go:"GO:0005634"(nucleus)|go:"GO:0005739"(mitochondrion)|go:"GO:0005789"(endoplasmic reticulum membrane)|go:"GO:0005829"(cytosol)|go:"GO:0006274"(DNA replication termination)|go:"GO:0010636"(positive regulation of mitochondrial fusion)|go:"GO:0016236"(macroautophagy)|go:"GO:0016320"(endoplasmic reticulum membrane fusion)|go:"GO:0016887"(ATP hydrolysis activity)|go:"GO:0019888"(protein phosphatase regulator activity)|go:"GO:0030433"(ubiquitin-dependent ERAD pathway)|go:"GO:0030894"(replisome)|go:"GO:0030970"(retrograde protein transport, ER to cytosol)|go:"GO:0031134"(sister chromatid biorientation)|go:"GO:0031593"(polyubiquitin modification-dependent protein binding)|go:"GO:0034098"(VCP-NPL4-UFD1 AAA ATPase complex)|go:"GO:0034517"(ribophagy)|go:"GO:0034727"(piecemeal microautophagy of the nucleus)|go:"GO:0036266"(Cdc48p-Npl4p-Vms1p AAA ATPase complex)|go:"GO:0042802"(identical protein binding)|go:"GO:0043130"(ubiquitin binding)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0043328"(protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway)|go:"GO:0043332"(mating projection tip)|go:"GO:0043624"|go:"GO:0046034"(ATP metabolic process)|go:"GO:0051228"(mitotic spindle disassembly)|go:"GO:0051974"(negative regulation of telomerase activity)|go:"GO:0070651"(nonfunctional rRNA decay)|go:"GO:0071629"(cytoplasm protein quality control by the ubiquitin-proteasome system)|go:"GO:0071630"(nuclear protein quality control by the ubiquitin-proteasome system)|go:"GO:0071712"(ER-associated misfolded protein catabolic process)|go:"GO:0072671"(mitochondria-associated ubiquitin-dependent protein catabolic process)|go:"GO:0097352"(autophagosome maturation)|go:"GO:0120174"(stress-induced homeostatically regulated protein degradation pathway)|go:"GO:0140603"(obsolete ATP hydrolysis activity)|go:"GO:1900182"(positive regulation of protein localization to nucleus)|go:"GO:1990112"(RQC complex)|go:"GO:1990116"(ribosome-associated ubiquitin-dependent protein catabolic process)|go:"GO:1990171"(SCF complex disassembly in response to cadmium stress)|go:"GO:2001168"(positive regulation of histone H2B ubiquitination)|interpro:IPR003338(AAA ATPase VAT, N-terminal)|interpro:IPR003593(AAA+ ATPase, core)|interpro:IPR003959(AAA ATPase, core)|interpro:IPR003960(AAA ATPase, conserved site)|interpro:IPR004201(Cell division protein 48, CDC48, domain 2)|interpro:IPR005938(AAA ATPase, CDC48)|interpro:IPR009010(Aspartate decarboxylase-like fold)|interpro:IPR015415(Vps4 oligomerisation, C-terminal)|interpro:IPR027417|interpro:IPR029067|interpro:IPR041569|rcsb pdb:6OA9|rcsb pdb:6OAA|rcsb pdb:6OAB|rcsb pdb:6OMB|rcsb pdb:6OPC|reactome:R-SCE-110320|reactome:R-SCE-3371511|reactome:R-SCE-532668|reactome:R-SCE-5358346|reactome:R-SCE-5689896|reactome:R-SCE-6798695|reactome:R-SCE-8876725	sgd:S000001410(RPL40A)|sgd:S000001802(RPL40B)|sgd:S000004157(RPS31)|sgd:S000003962(UBI4)|uniprotkb:P61864(see-also)|refseq:NP_012118.1|refseq:NP_013020.1|refseq:NP_013061.1|refseq:NP_013268.1|ensembl:YIL148W|ensembl:YKR094C|ensembl:YLR167W|go:"GO:0005515"(protein binding)|interpro:IPR000626(Ubiquitin)|cygd:YLR167w|go:"GO:0022625"(cytosolic large ribosomal subunit)|go:"GO:0005739"(mitochondrion)|go:"GO:0003735"(structural constituent of ribosome)|go:"GO:0016567"(protein ubiquitination)|go:"GO:0042254"(ribosome biogenesis)|go:"GO:0006412"(translation)|ensembl:YLL039C|rcsb pdb:1OTR|rcsb pdb:1Q0W|rcsb pdb:1WR1|rcsb pdb:1ZW7|rcsb pdb:2G3Q|go:"GO:0005634"(nucleus)|go:"GO:0006281"(DNA repair)|cygd:YIL148w|cygd:YKR094c|cygd:YLL039c|rcsb pdb:2JT4|rcsb pdb:2JWZ|rcsb pdb:3CMM|interpro:IPR019954|interpro:IPR019956|interpro:IPR019955|rcsb pdb:3L0W|rcsb pdb:3L10|rcsb pdb:3MHS|rcsb pdb:2KDI	wwpdb:6OA9(subset)|wwpdb:6OAA(subset)|wwpdb:6OAB(subset)	crc64:02ADDB9A227614D8	no-uniprot-update:obsolete protein	figure legend:Fig 1, Table S1|full coverage:Only protein-protein interactions|curation depth:imex curation	taxid:-1(in vitro)|taxid:-1(In vitro)	-	2019/07/13	2020/06/23	rogid:qM/04kWcyjkQ3QCa3WklyvhNigE559292	rogid:sUFDb7kGedoC/k80bI4sjOaMLHs4932	rigid:wX0IdG8fuVmAlLsUI4m14/3+b8Y	false	mutation:588-588	-	6	3	psi-mi:"MI:2287"(identification by structure determination)	psi-mi:"MI:2287"(identification by structure determination)
intact:EBI-19797	uniprotkb:P53044	dip:DIP-1549N|uniprotkb:P04838|uniprotkb:Q6LA96	intact:EBI-19997|uniprotkb:D6VUI5|uniprotkb:Q45U36|ensemblfungi:YGR048W	psi-mi:ubiq_yeast(display_short)|psi-mi:EBI-19797(display_long)|uniprotkb:UBI1(gene name)|psi-mi:UBI1(display_short)|uniprotkb:RPL40A(gene name synonym)|uniprotkb:YIL148W(locus name)|uniprotkb:UBI2(gene name)|psi-mi:UBI2(display_short)|uniprotkb:RPL40B(gene name synonym)|uniprotkb:YKR094C(locus name)|uniprotkb:UBI3(gene name)|psi-mi:UBI3(display_short)|uniprotkb:RPS31(gene name synonym)|uniprotkb:YLR167W(locus name)|uniprotkb:L9470.14(orf name)|uniprotkb:UBI4(gene name)|psi-mi:UBI4(display_short)|uniprotkb:SCD2(gene name synonym)|uniprotkb:YLL039C(locus name)	psi-mi:ufd1_yeast(display_long)|uniprotkb:UFD1(gene name)|psi-mi:UFD1(display_short)|uniprotkb:PIP3(gene name synonym)|uniprotkb:Polymerase-interacting protein 3(gene name synonym)|uniprotkb:YGR048W(locus name)	psi-mi:"MI:0096"(pull down)	Twomey et al. (2019)	pubmed:31249135|imex:IM-27726	taxid:4932(yeasx)|taxid:4932("Saccharomyces cerevisiae (Baker's yeast)")	taxid:559292(yeast)|taxid:559292(Saccharomyces cerevisiae)	psi-mi:"MI:0914"(association)	psi-mi:"MI:0465"(DIP)	intact:EBI-21915226|imex:IM-27726-3	-	psi-mi:"MI:1060"(spoke expansion)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0496"(bait)	psi-mi:"MI:0498"(prey)	psi-mi:"MI:0326"(protein)	psi-mi:"MI:0326"(protein)	sgd:S000001410(RPL40A)|sgd:S000001802(RPL40B)|sgd:S000004157(RPS31)|sgd:S000003962(UBI4)|uniprotkb:P61864(see-also)|refseq:NP_012118.1|refseq:NP_013020.1|refseq:NP_013061.1|refseq:NP_013268.1|ensembl:YIL148W|ensembl:YKR094C|ensembl:YLR167W|go:"GO:0005515"(protein binding)|interpro:IPR000626(Ubiquitin)|cygd:YLR167w|go:"GO:0022625"(cytosolic large ribosomal subunit)|go:"GO:0005739"(mitochondrion)|go:"GO:0003735"(structural constituent of ribosome)|go:"GO:0016567"(protein ubiquitination)|go:"GO:0042254"(ribosome biogenesis)|go:"GO:0006412"(translation)|ensembl:YLL039C|rcsb pdb:1OTR|rcsb pdb:1Q0W|rcsb pdb:1WR1|rcsb pdb:1ZW7|rcsb pdb:2G3Q|go:"GO:0005634"(nucleus)|go:"GO:0006281"(DNA repair)|cygd:YIL148w|cygd:YKR094c|cygd:YLL039c|rcsb pdb:2JT4|rcsb pdb:2JWZ|rcsb pdb:3CMM|interpro:IPR019954|interpro:IPR019956|interpro:IPR019955|rcsb pdb:3L0W|rcsb pdb:3L10|rcsb pdb:3MHS|rcsb pdb:2KDI	refseq:NP_011562.1|sgd:S000003280|go:"GO:0006274"(DNA replication termination)|go:"GO:0030433"(ubiquitin-dependent ERAD pathway)|go:"GO:0030894"(replisome)|go:"GO:0030970"(retrograde protein transport, ER to cytosol)|go:"GO:0031593"(polyubiquitin modification-dependent protein binding)|go:"GO:0034098"(VCP-NPL4-UFD1 AAA ATPase complex)|go:"GO:0043130"(ubiquitin binding)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0051974"(negative regulation of telomerase activity)|go:"GO:0070651"(nonfunctional rRNA decay)|go:"GO:0071629"(cytoplasm protein quality control by the ubiquitin-proteasome system)|go:"GO:0071712"(ER-associated misfolded protein catabolic process)|go:"GO:0072665"(protein localization to vacuole)|go:"GO:0072671"(mitochondria-associated ubiquitin-dependent protein catabolic process)|go:"GO:1900182"(positive regulation of protein localization to nucleus)|go:"GO:1990112"(RQC complex)|go:"GO:1990116"(ribosome-associated ubiquitin-dependent protein catabolic process)|interpro:IPR004854(Ubiquitin fusion degradation protein UFD1)|interpro:IPR042299|rcsb pdb:1ZC1|rcsb pdb:6JWJ|reactome:R-SCE-110320|ensemblfungi:YGR048W(gene)|ensemblfungi:YGR048W_mRNA(transcript)|go:"GO:0000837"(Doa10p ubiquitin ligase complex)|go:"GO:0000839"(Hrd1p ubiquitin ligase ERAD-L complex)|go:"GO:0005634"(nucleus)|go:"GO:0005829"(cytosol)|dip:DIP-1476N|mint:P53044	-	no-uniprot-update:obsolete protein	crc64:198E0CD48B863B98	figure legend:Fig 1c|full coverage:Only protein-protein interactions|curation depth:imex curation	taxid:-1(in vitro)|taxid:-1(In vitro)	-	2019/07/13	2019/07/14	rogid:sUFDb7kGedoC/k80bI4sjOaMLHs4932	rogid:u/YG6aRuJ38NLsxGkUsfM9nXAnU559292	rigid:w4bXG3L7sS4v7KL2EAu2UVtpTv8	false	-	-	-	-	psi-mi:"MI:0818"(molecular weight estimation by coomasie staining)	psi-mi:"MI:0818"(molecular weight estimation by coomasie staining)
intact:EBI-19797	uniprotkb:P33755	dip:DIP-1549N|uniprotkb:P04838|uniprotkb:Q6LA96	intact:EBI-12193|uniprotkb:D6VQG6|ensemblfungi:YBR170C	psi-mi:ubiq_yeast(display_short)|psi-mi:EBI-19797(display_long)|uniprotkb:UBI1(gene name)|psi-mi:UBI1(display_short)|uniprotkb:RPL40A(gene name synonym)|uniprotkb:YIL148W(locus name)|uniprotkb:UBI2(gene name)|psi-mi:UBI2(display_short)|uniprotkb:RPL40B(gene name synonym)|uniprotkb:YKR094C(locus name)|uniprotkb:UBI3(gene name)|psi-mi:UBI3(display_short)|uniprotkb:RPS31(gene name synonym)|uniprotkb:YLR167W(locus name)|uniprotkb:L9470.14(orf name)|uniprotkb:UBI4(gene name)|psi-mi:UBI4(display_short)|uniprotkb:SCD2(gene name synonym)|uniprotkb:YLL039C(locus name)	psi-mi:npl4_yeast(display_long)|uniprotkb:NPL4(gene name)|psi-mi:NPL4(display_short)|uniprotkb:YBR170C(locus name)|uniprotkb:YBR1231(orf name)|uniprotkb:HRD4(gene name synonym)|uniprotkb:HMG-CoA reductase degradation protein 4(gene name synonym)	psi-mi:"MI:0096"(pull down)	Twomey et al. (2019)	pubmed:31249135|imex:IM-27726	taxid:4932(yeasx)|taxid:4932("Saccharomyces cerevisiae (Baker's yeast)")	taxid:559292(yeast)|taxid:559292(Saccharomyces cerevisiae)	psi-mi:"MI:0914"(association)	psi-mi:"MI:0465"(DIP)	intact:EBI-21915226|imex:IM-27726-3	-	psi-mi:"MI:1060"(spoke expansion)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0496"(bait)	psi-mi:"MI:0498"(prey)	psi-mi:"MI:0326"(protein)	psi-mi:"MI:0326"(protein)	sgd:S000001410(RPL40A)|sgd:S000001802(RPL40B)|sgd:S000004157(RPS31)|sgd:S000003962(UBI4)|uniprotkb:P61864(see-also)|refseq:NP_012118.1|refseq:NP_013020.1|refseq:NP_013061.1|refseq:NP_013268.1|ensembl:YIL148W|ensembl:YKR094C|ensembl:YLR167W|go:"GO:0005515"(protein binding)|interpro:IPR000626(Ubiquitin)|cygd:YLR167w|go:"GO:0022625"(cytosolic large ribosomal subunit)|go:"GO:0005739"(mitochondrion)|go:"GO:0003735"(structural constituent of ribosome)|go:"GO:0016567"(protein ubiquitination)|go:"GO:0042254"(ribosome biogenesis)|go:"GO:0006412"(translation)|ensembl:YLL039C|rcsb pdb:1OTR|rcsb pdb:1Q0W|rcsb pdb:1WR1|rcsb pdb:1ZW7|rcsb pdb:2G3Q|go:"GO:0005634"(nucleus)|go:"GO:0006281"(DNA repair)|cygd:YIL148w|cygd:YKR094c|cygd:YLL039c|rcsb pdb:2JT4|rcsb pdb:2JWZ|rcsb pdb:3CMM|interpro:IPR019954|interpro:IPR019956|interpro:IPR019955|rcsb pdb:3L0W|rcsb pdb:3L10|rcsb pdb:3MHS|rcsb pdb:2KDI	ensemblfungi:YBR170C(gene)|ensemblfungi:YBR170C_mRNA(transcript)|go:"GO:0000837"(Doa10p ubiquitin ligase complex)|go:"GO:0000839"(Hrd1p ubiquitin ligase ERAD-L complex)|go:"GO:0005634"(nucleus)|go:"GO:0005737"(cytoplasm)|go:"GO:0006274"(DNA replication termination)|go:"GO:0006511"(ubiquitin-dependent protein catabolic process)|go:"GO:0030433"(ubiquitin-dependent ERAD pathway)|go:"GO:0030894"(replisome)|go:"GO:0030970"(retrograde protein transport, ER to cytosol)|go:"GO:0031625"(ubiquitin protein ligase binding)|go:"GO:0031965"(nuclear membrane)|go:"GO:0034098"(VCP-NPL4-UFD1 AAA ATPase complex)|go:"GO:0036266"(Cdc48p-Npl4p-Vms1p AAA ATPase complex)|go:"GO:0042175"(nuclear outer membrane-endoplasmic reticulum membrane network)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0051028"(mRNA transport)|go:"GO:0051228"(mitotic spindle disassembly)|go:"GO:0051974"(negative regulation of telomerase activity)|go:"GO:0070651"(nonfunctional rRNA decay)|go:"GO:0071629"(cytoplasm protein quality control by the ubiquitin-proteasome system)|go:"GO:0071712"(ER-associated misfolded protein catabolic process)|go:"GO:0072665"(protein localization to vacuole)|go:"GO:0072671"(mitochondria-associated ubiquitin-dependent protein catabolic process)|go:"GO:1900182"(positive regulation of protein localization to nucleus)|go:"GO:1990112"(RQC complex)|go:"GO:1990116"(ribosome-associated ubiquitin-dependent protein catabolic process)|interpro:IPR007716(NPL4, zinc-binding putative)|go:"GO:0043130"(ubiquitin binding)|interpro:IPR016563(Polyubiquitin-tagged protein recognition complex, Npl4 component)|interpro:IPR029071|interpro:IPR037518|rcsb pdb:6JWH|rcsb pdb:6JWI|rcsb pdb:6JWJ|interpro:IPR007717(NPL4)|rcsb pdb:6OA9|rcsb pdb:6OAA|reactome:R-SCE-110320|refseq:NP_009729.1|sgd:S000000374|dip:DIP-1475N|mint:P33755	-	no-uniprot-update:obsolete protein	crc64:6EF35D21338EE07E	figure legend:Fig 1c|full coverage:Only protein-protein interactions|curation depth:imex curation	taxid:-1(in vitro)|taxid:-1(In vitro)	-	2019/07/13	2019/07/14	rogid:sUFDb7kGedoC/k80bI4sjOaMLHs4932	rogid:2+0sYJtYCsEX5lm8Tk91hNDj8II559292	rigid:w4bXG3L7sS4v7KL2EAu2UVtpTv8	false	-	-	-	-	psi-mi:"MI:0818"(molecular weight estimation by coomasie staining)	psi-mi:"MI:0818"(molecular weight estimation by coomasie staining)
intact:EBI-19797	uniprotkb:P25694	dip:DIP-1549N|uniprotkb:P04838|uniprotkb:Q6LA96	intact:EBI-4308|ensemblfungi:YDL126C|uniprotkb:D6VRM4	psi-mi:ubiq_yeast(display_short)|psi-mi:EBI-19797(display_long)|uniprotkb:UBI1(gene name)|psi-mi:UBI1(display_short)|uniprotkb:RPL40A(gene name synonym)|uniprotkb:YIL148W(locus name)|uniprotkb:UBI2(gene name)|psi-mi:UBI2(display_short)|uniprotkb:RPL40B(gene name synonym)|uniprotkb:YKR094C(locus name)|uniprotkb:UBI3(gene name)|psi-mi:UBI3(display_short)|uniprotkb:RPS31(gene name synonym)|uniprotkb:YLR167W(locus name)|uniprotkb:L9470.14(orf name)|uniprotkb:UBI4(gene name)|psi-mi:UBI4(display_short)|uniprotkb:SCD2(gene name synonym)|uniprotkb:YLL039C(locus name)	psi-mi:cdc48_yeast(display_long)|uniprotkb:CDC48(gene name)|psi-mi:CDC48(display_short)|uniprotkb:Cell division cycle protein 48(gene name synonym)|uniprotkb:Transitional endoplasmic reticulum ATPase homolog(gene name synonym)|uniprotkb:YDL126C(locus name)	psi-mi:"MI:0096"(pull down)	Twomey et al. (2019)	pubmed:31249135|imex:IM-27726	taxid:4932(yeasx)|taxid:4932("Saccharomyces cerevisiae (Baker's yeast)")	taxid:559292(yeast)|taxid:559292(Saccharomyces cerevisiae)	psi-mi:"MI:0914"(association)	psi-mi:"MI:0465"(DIP)	intact:EBI-21915226|imex:IM-27726-3	-	psi-mi:"MI:1060"(spoke expansion)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0496"(bait)	psi-mi:"MI:0498"(prey)	psi-mi:"MI:0326"(protein)	psi-mi:"MI:0326"(protein)	sgd:S000001410(RPL40A)|sgd:S000001802(RPL40B)|sgd:S000004157(RPS31)|sgd:S000003962(UBI4)|uniprotkb:P61864(see-also)|refseq:NP_012118.1|refseq:NP_013020.1|refseq:NP_013061.1|refseq:NP_013268.1|ensembl:YIL148W|ensembl:YKR094C|ensembl:YLR167W|go:"GO:0005515"(protein binding)|interpro:IPR000626(Ubiquitin)|cygd:YLR167w|go:"GO:0022625"(cytosolic large ribosomal subunit)|go:"GO:0005739"(mitochondrion)|go:"GO:0003735"(structural constituent of ribosome)|go:"GO:0016567"(protein ubiquitination)|go:"GO:0042254"(ribosome biogenesis)|go:"GO:0006412"(translation)|ensembl:YLL039C|rcsb pdb:1OTR|rcsb pdb:1Q0W|rcsb pdb:1WR1|rcsb pdb:1ZW7|rcsb pdb:2G3Q|go:"GO:0005634"(nucleus)|go:"GO:0006281"(DNA repair)|cygd:YIL148w|cygd:YKR094c|cygd:YLL039c|rcsb pdb:2JT4|rcsb pdb:2JWZ|rcsb pdb:3CMM|interpro:IPR019954|interpro:IPR019956|interpro:IPR019955|rcsb pdb:3L0W|rcsb pdb:3L10|rcsb pdb:3MHS|rcsb pdb:2KDI	refseq:NP_010157.1|sgd:S000002284|ensemblfungi:YDL126C(gene)|ensemblfungi:YDL126C_mRNA(transcript)|go:"GO:0000837"(Doa10p ubiquitin ligase complex)|dip:DIP-2704N|mint:P25694|go:"GO:0000839"(Hrd1p ubiquitin ligase ERAD-L complex)|go:"GO:0005524"(ATP binding)|go:"GO:0005634"(nucleus)|go:"GO:0005739"(mitochondrion)|go:"GO:0005789"(endoplasmic reticulum membrane)|go:"GO:0005829"(cytosol)|go:"GO:0006274"(DNA replication termination)|go:"GO:0010636"(positive regulation of mitochondrial fusion)|go:"GO:0016236"(macroautophagy)|go:"GO:0016320"(endoplasmic reticulum membrane fusion)|go:"GO:0016887"(ATP hydrolysis activity)|go:"GO:0019888"(protein phosphatase regulator activity)|go:"GO:0030433"(ubiquitin-dependent ERAD pathway)|go:"GO:0030894"(replisome)|go:"GO:0030970"(retrograde protein transport, ER to cytosol)|go:"GO:0031134"(sister chromatid biorientation)|go:"GO:0031593"(polyubiquitin modification-dependent protein binding)|go:"GO:0034098"(VCP-NPL4-UFD1 AAA ATPase complex)|go:"GO:0034517"(ribophagy)|go:"GO:0034727"(piecemeal microautophagy of the nucleus)|go:"GO:0036266"(Cdc48p-Npl4p-Vms1p AAA ATPase complex)|go:"GO:0042802"(identical protein binding)|go:"GO:0043130"(ubiquitin binding)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0043328"(protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway)|go:"GO:0043332"(mating projection tip)|go:"GO:0043624"|go:"GO:0046034"(ATP metabolic process)|go:"GO:0051228"(mitotic spindle disassembly)|go:"GO:0051974"(negative regulation of telomerase activity)|go:"GO:0070651"(nonfunctional rRNA decay)|go:"GO:0071629"(cytoplasm protein quality control by the ubiquitin-proteasome system)|go:"GO:0071630"(nuclear protein quality control by the ubiquitin-proteasome system)|go:"GO:0071712"(ER-associated misfolded protein catabolic process)|go:"GO:0072671"(mitochondria-associated ubiquitin-dependent protein catabolic process)|go:"GO:0097352"(autophagosome maturation)|go:"GO:0120174"(stress-induced homeostatically regulated protein degradation pathway)|go:"GO:0140603"(obsolete ATP hydrolysis activity)|go:"GO:1900182"(positive regulation of protein localization to nucleus)|go:"GO:1990112"(RQC complex)|go:"GO:1990116"(ribosome-associated ubiquitin-dependent protein catabolic process)|go:"GO:1990171"(SCF complex disassembly in response to cadmium stress)|go:"GO:2001168"(positive regulation of histone H2B ubiquitination)|interpro:IPR003338(AAA ATPase VAT, N-terminal)|interpro:IPR003593(AAA+ ATPase, core)|interpro:IPR003959(AAA ATPase, core)|interpro:IPR003960(AAA ATPase, conserved site)|interpro:IPR004201(Cell division protein 48, CDC48, domain 2)|interpro:IPR005938(AAA ATPase, CDC48)|interpro:IPR009010(Aspartate decarboxylase-like fold)|interpro:IPR015415(Vps4 oligomerisation, C-terminal)|interpro:IPR027417|interpro:IPR029067|interpro:IPR041569|rcsb pdb:6OA9|rcsb pdb:6OAA|rcsb pdb:6OAB|rcsb pdb:6OMB|rcsb pdb:6OPC|reactome:R-SCE-110320|reactome:R-SCE-3371511|reactome:R-SCE-532668|reactome:R-SCE-5358346|reactome:R-SCE-5689896|reactome:R-SCE-6798695|reactome:R-SCE-8876725	-	no-uniprot-update:obsolete protein	crc64:02ADDB9A227614D8	figure legend:Fig 1c|full coverage:Only protein-protein interactions|curation depth:imex curation	taxid:-1(in vitro)|taxid:-1(In vitro)	-	2019/07/13	2019/07/14	rogid:sUFDb7kGedoC/k80bI4sjOaMLHs4932	rogid:qM/04kWcyjkQ3QCa3WklyvhNigE559292	rigid:w4bXG3L7sS4v7KL2EAu2UVtpTv8	false	-	mutation:588-588	-	-	psi-mi:"MI:0818"(molecular weight estimation by coomasie staining)	psi-mi:"MI:0818"(molecular weight estimation by coomasie staining)
intact:EBI-19797	uniprotkb:P25694	dip:DIP-1549N|uniprotkb:P04838|uniprotkb:Q6LA96	intact:EBI-4308|ensemblfungi:YDL126C|uniprotkb:D6VRM4	psi-mi:ubiq_yeast(display_short)|psi-mi:EBI-19797(display_long)|uniprotkb:UBI1(gene name)|psi-mi:UBI1(display_short)|uniprotkb:RPL40A(gene name synonym)|uniprotkb:YIL148W(locus name)|uniprotkb:UBI2(gene name)|psi-mi:UBI2(display_short)|uniprotkb:RPL40B(gene name synonym)|uniprotkb:YKR094C(locus name)|uniprotkb:UBI3(gene name)|psi-mi:UBI3(display_short)|uniprotkb:RPS31(gene name synonym)|uniprotkb:YLR167W(locus name)|uniprotkb:L9470.14(orf name)|uniprotkb:UBI4(gene name)|psi-mi:UBI4(display_short)|uniprotkb:SCD2(gene name synonym)|uniprotkb:YLL039C(locus name)	psi-mi:cdc48_yeast(display_long)|uniprotkb:CDC48(gene name)|psi-mi:CDC48(display_short)|uniprotkb:Cell division cycle protein 48(gene name synonym)|uniprotkb:Transitional endoplasmic reticulum ATPase homolog(gene name synonym)|uniprotkb:YDL126C(locus name)	psi-mi:"MI:0030"(cross-linking study)	Twomey et al. (2019)	pubmed:31249135|imex:IM-27726	taxid:4932(yeasx)|taxid:4932("Saccharomyces cerevisiae (Baker's yeast)")	taxid:559292(yeast)|taxid:559292(Saccharomyces cerevisiae)	psi-mi:"MI:0407"(direct interaction)	psi-mi:"MI:0465"(DIP)	intact:EBI-21915240|imex:IM-27726-5	-	-	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0498"(prey)	psi-mi:"MI:0496"(bait)	psi-mi:"MI:0326"(protein)	psi-mi:"MI:0326"(protein)	sgd:S000001410(RPL40A)|sgd:S000001802(RPL40B)|sgd:S000004157(RPS31)|sgd:S000003962(UBI4)|uniprotkb:P61864(see-also)|refseq:NP_012118.1|refseq:NP_013020.1|refseq:NP_013061.1|refseq:NP_013268.1|ensembl:YIL148W|ensembl:YKR094C|ensembl:YLR167W|go:"GO:0005515"(protein binding)|interpro:IPR000626(Ubiquitin)|cygd:YLR167w|go:"GO:0022625"(cytosolic large ribosomal subunit)|go:"GO:0005739"(mitochondrion)|go:"GO:0003735"(structural constituent of ribosome)|go:"GO:0016567"(protein ubiquitination)|go:"GO:0042254"(ribosome biogenesis)|go:"GO:0006412"(translation)|ensembl:YLL039C|rcsb pdb:1OTR|rcsb pdb:1Q0W|rcsb pdb:1WR1|rcsb pdb:1ZW7|rcsb pdb:2G3Q|go:"GO:0005634"(nucleus)|go:"GO:0006281"(DNA repair)|cygd:YIL148w|cygd:YKR094c|cygd:YLL039c|rcsb pdb:2JT4|rcsb pdb:2JWZ|rcsb pdb:3CMM|interpro:IPR019954|interpro:IPR019956|interpro:IPR019955|rcsb pdb:3L0W|rcsb pdb:3L10|rcsb pdb:3MHS|rcsb pdb:2KDI	refseq:NP_010157.1|sgd:S000002284|ensemblfungi:YDL126C(gene)|ensemblfungi:YDL126C_mRNA(transcript)|go:"GO:0000837"(Doa10p ubiquitin ligase complex)|dip:DIP-2704N|mint:P25694|go:"GO:0000839"(Hrd1p ubiquitin ligase ERAD-L complex)|go:"GO:0005524"(ATP binding)|go:"GO:0005634"(nucleus)|go:"GO:0005739"(mitochondrion)|go:"GO:0005789"(endoplasmic reticulum membrane)|go:"GO:0005829"(cytosol)|go:"GO:0006274"(DNA replication termination)|go:"GO:0010636"(positive regulation of mitochondrial fusion)|go:"GO:0016236"(macroautophagy)|go:"GO:0016320"(endoplasmic reticulum membrane fusion)|go:"GO:0016887"(ATP hydrolysis activity)|go:"GO:0019888"(protein phosphatase regulator activity)|go:"GO:0030433"(ubiquitin-dependent ERAD pathway)|go:"GO:0030894"(replisome)|go:"GO:0030970"(retrograde protein transport, ER to cytosol)|go:"GO:0031134"(sister chromatid biorientation)|go:"GO:0031593"(polyubiquitin modification-dependent protein binding)|go:"GO:0034098"(VCP-NPL4-UFD1 AAA ATPase complex)|go:"GO:0034517"(ribophagy)|go:"GO:0034727"(piecemeal microautophagy of the nucleus)|go:"GO:0036266"(Cdc48p-Npl4p-Vms1p AAA ATPase complex)|go:"GO:0042802"(identical protein binding)|go:"GO:0043130"(ubiquitin binding)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0043328"(protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway)|go:"GO:0043332"(mating projection tip)|go:"GO:0043624"|go:"GO:0046034"(ATP metabolic process)|go:"GO:0051228"(mitotic spindle disassembly)|go:"GO:0051974"(negative regulation of telomerase activity)|go:"GO:0070651"(nonfunctional rRNA decay)|go:"GO:0071629"(cytoplasm protein quality control by the ubiquitin-proteasome system)|go:"GO:0071630"(nuclear protein quality control by the ubiquitin-proteasome system)|go:"GO:0071712"(ER-associated misfolded protein catabolic process)|go:"GO:0072671"(mitochondria-associated ubiquitin-dependent protein catabolic process)|go:"GO:0097352"(autophagosome maturation)|go:"GO:0120174"(stress-induced homeostatically regulated protein degradation pathway)|go:"GO:0140603"(obsolete ATP hydrolysis activity)|go:"GO:1900182"(positive regulation of protein localization to nucleus)|go:"GO:1990112"(RQC complex)|go:"GO:1990116"(ribosome-associated ubiquitin-dependent protein catabolic process)|go:"GO:1990171"(SCF complex disassembly in response to cadmium stress)|go:"GO:2001168"(positive regulation of histone H2B ubiquitination)|interpro:IPR003338(AAA ATPase VAT, N-terminal)|interpro:IPR003593(AAA+ ATPase, core)|interpro:IPR003959(AAA ATPase, core)|interpro:IPR003960(AAA ATPase, conserved site)|interpro:IPR004201(Cell division protein 48, CDC48, domain 2)|interpro:IPR005938(AAA ATPase, CDC48)|interpro:IPR009010(Aspartate decarboxylase-like fold)|interpro:IPR015415(Vps4 oligomerisation, C-terminal)|interpro:IPR027417|interpro:IPR029067|interpro:IPR041569|rcsb pdb:6OA9|rcsb pdb:6OAA|rcsb pdb:6OAB|rcsb pdb:6OMB|rcsb pdb:6OPC|reactome:R-SCE-110320|reactome:R-SCE-3371511|reactome:R-SCE-532668|reactome:R-SCE-5358346|reactome:R-SCE-5689896|reactome:R-SCE-6798695|reactome:R-SCE-8876725	-	no-uniprot-update:obsolete protein	crc64:02ADDB9A227614D8	figure legend:Fig 4c|full coverage:Only protein-protein interactions|curation depth:imex curation	taxid:-1(in vitro)|taxid:-1(In vitro)	-	2019/07/13	2019/07/14	rogid:sUFDb7kGedoC/k80bI4sjOaMLHs4932	rogid:qM/04kWcyjkQ3QCa3WklyvhNigE559292	rigid:/QuYx/bTYSgsIjB7QIykWdO4Jaw	false	protein modification:1-2	flag tag:c-c|unnatural residue:602-602	-	-	psi-mi:"MI:0396"(predetermined participant)|psi-mi:"MI:0658"(multidimensional protein identification technology)	psi-mi:"MI:0396"(predetermined participant)|psi-mi:"MI:0658"(multidimensional protein identification technology)