TABLE 1 

Interacting proteins identified by AP-MS for ACBD3, TBC1D22A, TBC1D22B, and PI4KIIIba

BaitCa2+Accession
no.
Gene
designation
Protein nameZ
score
Replicate
count sum
ACBD3 NS15826852ACBD3Golgi resident protein GCP6023.5699
ACBD3 NS22507409TBC1D22ATBC1 domain family member 22A23.513
ACBD3 NS154816184TMEM55BTransmembrane protein 55B isoform 219.511
ACBD3 NS311771621PI4KBPhosphatidylinositol 4-kinase beta isoform 215.65
ACBD3 CS15826852ACBD3Golgi resident protein GCP6023.5587
ACBD3 CS154816184TMEM55BTransmembrane protein 55B isoform 219.56
ACBD3 CS149944715PPM1HProtein phosphatase 1H15.614
ACBD3 CS22507409TBC1D22ATBC1 domain family member 22A11.712
ACBD3 CS311771621PI4KBPhosphatidylinositol 4-kinase beta isoform 27.86
ACBD3 NS+15826852ACBD3Golgi resident protein GCP6023.5701
ACBD3 NS+148596984GOLGB1Golgin subfamily B member 123.562
ACBD3 NS+83641874CPVLProbable serine carboxypeptidase CPVL precursor23.521
ACBD3 NS+154816184TMEM55BTransmembrane protein 55B isoform 223.517
ACBD3 NS+11386135BCKDHA2-Oxoisovalerate dehydrogenase subunit alpha, mitochondrial isoform 1 precursor15.627
ACBD3 NS+34101272BCKDHB2-Oxoisovalerate dehydrogenase subunit beta, mitochondrial precursor15.613
ACBD3 NS+38026892ALG6Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase precursor15.612
ACBD3 NS+19923748DLSTDihydrolipoyllysine residue succinyltransferase component of 2-oxoglutarate
dehydrogenase complex, mitochondrial isoform 1 precursor
15.68
ACBD3 NS+124494254PA2G4Proliferation-associated protein 2G411.77
ACBD3 NS+7019485PDCD6Programmed cell death protein 611.77
ACBD3 NS+311771621PI4KBPhosphatidylinositol 4-kinase beta isoform 211.76
ACBD3 NS+6912582PEF1Peflin11.76
ACBD3 NS+55741641KIDINS220Kinase D-interacting substrate of 220 kDa7.84
ACBD3 NS+38679884SRISorcin isoform b7.83
ACBD3 CS+15826852ACBD3Golgi resident protein GCP6023.5842
ACBD3 CS+83641874CPVLProbable serine carboxypeptidase CPVL precursor23.524
ACBD3 CS+149944715PPM1HProtein phosphatase 1H23.516
ACBD3 CS+311771621PI4KBPhosphatidylinositol 4-kinase beta isoform 219.518
ACBD3 CS+154816184TMEM55BTransmembrane protein 55B isoform 219.511
ACBD3 CS+56549147STEAP3Metalloreductase STEAP3 isoform b15.614
ACBD3 CS+4504805BLZF1Golgin-4515.610
ACBD3 CS+38026892ALG6Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3- glucosyltransferase precursor11.712
ACBD3 CS+22507409TBC1D22ATBC1 domain family member 22A11.77
ACBD3 CS+19923748DLSTDihydrolipoyllysine residue succinyltransferase component of 2-oxoglutarate
dehydrogenase complex, mitochondrial isoform 1 precursor
7.89
ACBD3 CS+34101272BCKDHB2-Oxoisovalerate dehydrogenase subunit beta, mitochondrial precursor7.86
ACBD3 CS+40789249DARS2Aspartyl-tRNA synthetase, mitochondrial7.83
ACBD3 CS+148839335DPY19L1Protein Dpy-19 homolog 17.82
ACBD3 CS+11559925XPNPEP3Probable Xaa–Pro aminopeptidase 3 isoform 17.82
TBC1D22A22507409TBC1D22ATBC1 domain family member 22A23.5538
TBC1D22A15826852ACBD3Golgi resident protein GCP6023.542
TBC1D22A4506583RPA1Replication protein A 70-kDa DNA binding subunit11.736
TBC1D22A4506587RPA3Replication protein A 14-kDa subunit11.714
TBC1D22A4506585RPA2Replication protein A 32-kDa subunit11.76
TBC1D22A17999541VPS35Vacuolar protein sorting- associated protein 357.810
TBC1D22A124494254PA2G4Proliferation-associated protein 2G47.88
TBC1D22A14211889DPY30Protein Dpy-30 homolog7.86
TBC1D22A17978519VPS26AVacuolar protein sorting- associated protein 26A isoform 17.83
TBC1D22A23397429EIF3MEukaryotic translation initiation factor 3 subunit M7.83
TBC1D22B40068063TBC1D22BTBC1 domain family member 22B23.51,575
TBC1D22B15826852ACBD3Golgi resident protein GCP6023.5117
TBC1D22B198041662PYCRLPyrroline-5-carboxylate reductase 36.75
TBC1D22B4505067MAD2L1Mitotic spindle assembly checkpoint protein MAD2A6.75
TBC1D22B150378533USP7Ubiquitin carboxyl-terminal hydrolase 76.74
TBC1D22B51479145ARFGEF1Brefeldin A-inhibited guanine nucleotide exchange protein 16.74
PI4KB311771621PI4KBPhosphatidylinositol 4-kinase beta isoform 223.51,686
PI4KB15826852ACBD3Golgi resident protein GCP6023.535
PI4KB284807150GBAGlucosylceramidase isoform 218.823
PI4KB294832006PPP2R2ASerine/threonine-protein phosphatase 2A 55-kDa regulatory subunit B alpha isoform 214.17
PI4KB14141170MTA2Metastasis-associated protein MTA214.16
PI4KB154350213C10orf76UPF0668 protein C10orf769.417
PI4KB27363458LRFN4Leucine-rich repeat and fibronectin type III domain-containing protein 4 precursor9.413
  • a Interacting proteins identified by AP-MS for ACBD3, TBC1D22A, TBC1D22B, and PI4KIIIb were weighted by Z score of the peptide counts. Proteins are listed here with replicate Z scores and peptide counts in the experimental set with a minimum of n = 5 biological replicates and were scored against a background set of 550 unrelated picornaviral protein AP-MS experiments, excluding the 3A protein itself (Materials and Methods). Shown here are the top-scoring proteins that appeared in at least two replicate experiments and with >1 count in at least one experiment; a full Z score table is provided in Table S1, Tab SI.4 in the supplemental material. The major interacting proteins for ACBD3 included TBC1D22A and PI4KB, as well as PPM1H, TMEM55B isoform 2, CPVL, and GOLGB1. Reciprocal AP-MS experiments with TBC1D22A, its closely related isoform TBC1D22B, and PI4KB confirmed interaction with ACBD3. Proteins are C-terminally StrepII-tagged (CS) unless otherwise noted as N-terminally tagged (NS).