as160 tbc1d4 Search Results


tbc1d4  (Proteintech)
93
Proteintech tbc1d4
(A, B) Retromer interactions with TBC GAP and DENND GEF proteins across the human proteome. VPS26A-VPS35 and VPS29-VPS35 assemblies or individual VPS29, VPS26A and VPS35 proteins were screened against all human proteins with TBC and DENN domains using AlphaFold2. The confidence of potential interactors was scored based on the sum of the interfacial PTM score (iPTM) averaged from three models, pDOCKQ and SPOC scores. In TBC domain GAPs, TBC1D5 and TBC1D13 shows high confidence. In DENN domain GEFs, DENND4A and DENND4C were confidently predicted to bind to VPS29/Retromer. Others found to possess a PL motif but show low confidence in association with VPS29 binding are TBC1D1, <t>TBC1D4</t> and DENND11. (C) GFP based co-immunoprecipitation (co-IP) of GFP-TBC1D1, GFP-TBC1D4 or GFP-TBC1D13 after transient transfection in HEK293T cells. Co-expression of GFP-TBC1D1 with mCherry-TBC1D4 increased pull-down of Retromer complex subunits. (D, E) GFP based co-IP after transient transfection in HEK293T cells of wild-type (WT) and PL interacting-motive mutant versions of GFP-TBC1D1 (P87A) and mCherry-TBC1D4 (P15A). Quantitation and statistical analysis of relative band intensity for the indicated proteins normalized to GFP band intensity. n = 3 independent experiments. T-test analysis, data presented as mean values relative to WT and error bars represent SD. (F) Schematic summarizing the interactions of Retromer with the identified TBC GAPs and DENND GEFs and the similarity with binding to the FAM21 subunit of the WASH complex and the RidL protein from legionella. The intramolecular occlusion of the equivalent binding site in VPS29 when assembled in the Retriever complex prevents Retriever from binding to any of these proteins through these specific mechanisms.
Tbc1d4, supplied by Proteintech, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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antiphospho-tbc1d4ser704  (Capra Science)
90
Capra Science antiphospho-tbc1d4ser704
(A, B) Retromer interactions with TBC GAP and DENND GEF proteins across the human proteome. VPS26A-VPS35 and VPS29-VPS35 assemblies or individual VPS29, VPS26A and VPS35 proteins were screened against all human proteins with TBC and DENN domains using AlphaFold2. The confidence of potential interactors was scored based on the sum of the interfacial PTM score (iPTM) averaged from three models, pDOCKQ and SPOC scores. In TBC domain GAPs, TBC1D5 and TBC1D13 shows high confidence. In DENN domain GEFs, DENND4A and DENND4C were confidently predicted to bind to VPS29/Retromer. Others found to possess a PL motif but show low confidence in association with VPS29 binding are TBC1D1, <t>TBC1D4</t> and DENND11. (C) GFP based co-immunoprecipitation (co-IP) of GFP-TBC1D1, GFP-TBC1D4 or GFP-TBC1D13 after transient transfection in HEK293T cells. Co-expression of GFP-TBC1D1 with mCherry-TBC1D4 increased pull-down of Retromer complex subunits. (D, E) GFP based co-IP after transient transfection in HEK293T cells of wild-type (WT) and PL interacting-motive mutant versions of GFP-TBC1D1 (P87A) and mCherry-TBC1D4 (P15A). Quantitation and statistical analysis of relative band intensity for the indicated proteins normalized to GFP band intensity. n = 3 independent experiments. T-test analysis, data presented as mean values relative to WT and error bars represent SD. (F) Schematic summarizing the interactions of Retromer with the identified TBC GAPs and DENND GEFs and the similarity with binding to the FAM21 subunit of the WASH complex and the RidL protein from legionella. The intramolecular occlusion of the equivalent binding site in VPS29 when assembled in the Retriever complex prevents Retriever from binding to any of these proteins through these specific mechanisms.
Antiphospho Tbc1d4ser704, supplied by Capra Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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national center for biotechnology information amino acid sequence database  (Biotechnology Information)
90
Biotechnology Information national center for biotechnology information amino acid sequence database
(A, B) Retromer interactions with TBC GAP and DENND GEF proteins across the human proteome. VPS26A-VPS35 and VPS29-VPS35 assemblies or individual VPS29, VPS26A and VPS35 proteins were screened against all human proteins with TBC and DENN domains using AlphaFold2. The confidence of potential interactors was scored based on the sum of the interfacial PTM score (iPTM) averaged from three models, pDOCKQ and SPOC scores. In TBC domain GAPs, TBC1D5 and TBC1D13 shows high confidence. In DENN domain GEFs, DENND4A and DENND4C were confidently predicted to bind to VPS29/Retromer. Others found to possess a PL motif but show low confidence in association with VPS29 binding are TBC1D1, <t>TBC1D4</t> and DENND11. (C) GFP based co-immunoprecipitation (co-IP) of GFP-TBC1D1, GFP-TBC1D4 or GFP-TBC1D13 after transient transfection in HEK293T cells. Co-expression of GFP-TBC1D1 with mCherry-TBC1D4 increased pull-down of Retromer complex subunits. (D, E) GFP based co-IP after transient transfection in HEK293T cells of wild-type (WT) and PL interacting-motive mutant versions of GFP-TBC1D1 (P87A) and mCherry-TBC1D4 (P15A). Quantitation and statistical analysis of relative band intensity for the indicated proteins normalized to GFP band intensity. n = 3 independent experiments. T-test analysis, data presented as mean values relative to WT and error bars represent SD. (F) Schematic summarizing the interactions of Retromer with the identified TBC GAPs and DENND GEFs and the similarity with binding to the FAM21 subunit of the WASH complex and the RidL protein from legionella. The intramolecular occlusion of the equivalent binding site in VPS29 when assembled in the Retriever complex prevents Retriever from binding to any of these proteins through these specific mechanisms.
National Center For Biotechnology Information Amino Acid Sequence Database, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 90 stars, based on 1 article reviews
national center for biotechnology information amino acid sequence database - by Bioz Stars, 2026-02
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expression vector containing cdna encoding as160 (tbc1d4) fused to halotag (pfn21aa0603)  (Promega)
90
Promega expression vector containing cdna encoding as160 (tbc1d4) fused to halotag (pfn21aa0603)
(A, B) Retromer interactions with TBC GAP and DENND GEF proteins across the human proteome. VPS26A-VPS35 and VPS29-VPS35 assemblies or individual VPS29, VPS26A and VPS35 proteins were screened against all human proteins with TBC and DENN domains using AlphaFold2. The confidence of potential interactors was scored based on the sum of the interfacial PTM score (iPTM) averaged from three models, pDOCKQ and SPOC scores. In TBC domain GAPs, TBC1D5 and TBC1D13 shows high confidence. In DENN domain GEFs, DENND4A and DENND4C were confidently predicted to bind to VPS29/Retromer. Others found to possess a PL motif but show low confidence in association with VPS29 binding are TBC1D1, <t>TBC1D4</t> and DENND11. (C) GFP based co-immunoprecipitation (co-IP) of GFP-TBC1D1, GFP-TBC1D4 or GFP-TBC1D13 after transient transfection in HEK293T cells. Co-expression of GFP-TBC1D1 with mCherry-TBC1D4 increased pull-down of Retromer complex subunits. (D, E) GFP based co-IP after transient transfection in HEK293T cells of wild-type (WT) and PL interacting-motive mutant versions of GFP-TBC1D1 (P87A) and mCherry-TBC1D4 (P15A). Quantitation and statistical analysis of relative band intensity for the indicated proteins normalized to GFP band intensity. n = 3 independent experiments. T-test analysis, data presented as mean values relative to WT and error bars represent SD. (F) Schematic summarizing the interactions of Retromer with the identified TBC GAPs and DENND GEFs and the similarity with binding to the FAM21 subunit of the WASH complex and the RidL protein from legionella. The intramolecular occlusion of the equivalent binding site in VPS29 when assembled in the Retriever complex prevents Retriever from binding to any of these proteins through these specific mechanisms.
Expression Vector Containing Cdna Encoding As160 (Tbc1d4) Fused To Halotag (Pfn21aa0603), supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/expression vector containing cdna encoding as160 (tbc1d4) fused to halotag (pfn21aa0603)/product/Promega
Average 90 stars, based on 1 article reviews
expression vector containing cdna encoding as160 (tbc1d4) fused to halotag (pfn21aa0603) - by Bioz Stars, 2026-02
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heterozygous thr649ala-as160/tbc1d4 knock-in mice  (TaconicArtemis gmbh)
90
TaconicArtemis gmbh heterozygous thr649ala-as160/tbc1d4 knock-in mice
(A, B) Retromer interactions with TBC GAP and DENND GEF proteins across the human proteome. VPS26A-VPS35 and VPS29-VPS35 assemblies or individual VPS29, VPS26A and VPS35 proteins were screened against all human proteins with TBC and DENN domains using AlphaFold2. The confidence of potential interactors was scored based on the sum of the interfacial PTM score (iPTM) averaged from three models, pDOCKQ and SPOC scores. In TBC domain GAPs, TBC1D5 and TBC1D13 shows high confidence. In DENN domain GEFs, DENND4A and DENND4C were confidently predicted to bind to VPS29/Retromer. Others found to possess a PL motif but show low confidence in association with VPS29 binding are TBC1D1, <t>TBC1D4</t> and DENND11. (C) GFP based co-immunoprecipitation (co-IP) of GFP-TBC1D1, GFP-TBC1D4 or GFP-TBC1D13 after transient transfection in HEK293T cells. Co-expression of GFP-TBC1D1 with mCherry-TBC1D4 increased pull-down of Retromer complex subunits. (D, E) GFP based co-IP after transient transfection in HEK293T cells of wild-type (WT) and PL interacting-motive mutant versions of GFP-TBC1D1 (P87A) and mCherry-TBC1D4 (P15A). Quantitation and statistical analysis of relative band intensity for the indicated proteins normalized to GFP band intensity. n = 3 independent experiments. T-test analysis, data presented as mean values relative to WT and error bars represent SD. (F) Schematic summarizing the interactions of Retromer with the identified TBC GAPs and DENND GEFs and the similarity with binding to the FAM21 subunit of the WASH complex and the RidL protein from legionella. The intramolecular occlusion of the equivalent binding site in VPS29 when assembled in the Retriever complex prevents Retriever from binding to any of these proteins through these specific mechanisms.
Heterozygous Thr649ala As160/Tbc1d4 Knock In Mice, supplied by TaconicArtemis gmbh, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/heterozygous thr649ala-as160/tbc1d4 knock-in mice/product/TaconicArtemis gmbh
Average 90 stars, based on 1 article reviews
heterozygous thr649ala-as160/tbc1d4 knock-in mice - by Bioz Stars, 2026-02
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tbc domain family, member 4 (tbc1d4; also known as as160)  (EVJ Ltd)
90
EVJ Ltd tbc domain family, member 4 (tbc1d4; also known as as160)
(A, B) Retromer interactions with TBC GAP and DENND GEF proteins across the human proteome. VPS26A-VPS35 and VPS29-VPS35 assemblies or individual VPS29, VPS26A and VPS35 proteins were screened against all human proteins with TBC and DENN domains using AlphaFold2. The confidence of potential interactors was scored based on the sum of the interfacial PTM score (iPTM) averaged from three models, pDOCKQ and SPOC scores. In TBC domain GAPs, TBC1D5 and TBC1D13 shows high confidence. In DENN domain GEFs, DENND4A and DENND4C were confidently predicted to bind to VPS29/Retromer. Others found to possess a PL motif but show low confidence in association with VPS29 binding are TBC1D1, <t>TBC1D4</t> and DENND11. (C) GFP based co-immunoprecipitation (co-IP) of GFP-TBC1D1, GFP-TBC1D4 or GFP-TBC1D13 after transient transfection in HEK293T cells. Co-expression of GFP-TBC1D1 with mCherry-TBC1D4 increased pull-down of Retromer complex subunits. (D, E) GFP based co-IP after transient transfection in HEK293T cells of wild-type (WT) and PL interacting-motive mutant versions of GFP-TBC1D1 (P87A) and mCherry-TBC1D4 (P15A). Quantitation and statistical analysis of relative band intensity for the indicated proteins normalized to GFP band intensity. n = 3 independent experiments. T-test analysis, data presented as mean values relative to WT and error bars represent SD. (F) Schematic summarizing the interactions of Retromer with the identified TBC GAPs and DENND GEFs and the similarity with binding to the FAM21 subunit of the WASH complex and the RidL protein from legionella. The intramolecular occlusion of the equivalent binding site in VPS29 when assembled in the Retriever complex prevents Retriever from binding to any of these proteins through these specific mechanisms.
Tbc Domain Family, Member 4 (Tbc1d4; Also Known As As160), supplied by EVJ Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 90 stars, based on 1 article reviews
tbc domain family, member 4 (tbc1d4; also known as as160) - by Bioz Stars, 2026-02
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Image Search Results


(A, B) Retromer interactions with TBC GAP and DENND GEF proteins across the human proteome. VPS26A-VPS35 and VPS29-VPS35 assemblies or individual VPS29, VPS26A and VPS35 proteins were screened against all human proteins with TBC and DENN domains using AlphaFold2. The confidence of potential interactors was scored based on the sum of the interfacial PTM score (iPTM) averaged from three models, pDOCKQ and SPOC scores. In TBC domain GAPs, TBC1D5 and TBC1D13 shows high confidence. In DENN domain GEFs, DENND4A and DENND4C were confidently predicted to bind to VPS29/Retromer. Others found to possess a PL motif but show low confidence in association with VPS29 binding are TBC1D1, TBC1D4 and DENND11. (C) GFP based co-immunoprecipitation (co-IP) of GFP-TBC1D1, GFP-TBC1D4 or GFP-TBC1D13 after transient transfection in HEK293T cells. Co-expression of GFP-TBC1D1 with mCherry-TBC1D4 increased pull-down of Retromer complex subunits. (D, E) GFP based co-IP after transient transfection in HEK293T cells of wild-type (WT) and PL interacting-motive mutant versions of GFP-TBC1D1 (P87A) and mCherry-TBC1D4 (P15A). Quantitation and statistical analysis of relative band intensity for the indicated proteins normalized to GFP band intensity. n = 3 independent experiments. T-test analysis, data presented as mean values relative to WT and error bars represent SD. (F) Schematic summarizing the interactions of Retromer with the identified TBC GAPs and DENND GEFs and the similarity with binding to the FAM21 subunit of the WASH complex and the RidL protein from legionella. The intramolecular occlusion of the equivalent binding site in VPS29 when assembled in the Retriever complex prevents Retriever from binding to any of these proteins through these specific mechanisms.

Journal: bioRxiv

Article Title: Mapping the endosomal proximity proteome reveals Retromer as a hub for RAB GTPase regulation

doi: 10.1101/2024.11.22.622898

Figure Lengend Snippet: (A, B) Retromer interactions with TBC GAP and DENND GEF proteins across the human proteome. VPS26A-VPS35 and VPS29-VPS35 assemblies or individual VPS29, VPS26A and VPS35 proteins were screened against all human proteins with TBC and DENN domains using AlphaFold2. The confidence of potential interactors was scored based on the sum of the interfacial PTM score (iPTM) averaged from three models, pDOCKQ and SPOC scores. In TBC domain GAPs, TBC1D5 and TBC1D13 shows high confidence. In DENN domain GEFs, DENND4A and DENND4C were confidently predicted to bind to VPS29/Retromer. Others found to possess a PL motif but show low confidence in association with VPS29 binding are TBC1D1, TBC1D4 and DENND11. (C) GFP based co-immunoprecipitation (co-IP) of GFP-TBC1D1, GFP-TBC1D4 or GFP-TBC1D13 after transient transfection in HEK293T cells. Co-expression of GFP-TBC1D1 with mCherry-TBC1D4 increased pull-down of Retromer complex subunits. (D, E) GFP based co-IP after transient transfection in HEK293T cells of wild-type (WT) and PL interacting-motive mutant versions of GFP-TBC1D1 (P87A) and mCherry-TBC1D4 (P15A). Quantitation and statistical analysis of relative band intensity for the indicated proteins normalized to GFP band intensity. n = 3 independent experiments. T-test analysis, data presented as mean values relative to WT and error bars represent SD. (F) Schematic summarizing the interactions of Retromer with the identified TBC GAPs and DENND GEFs and the similarity with binding to the FAM21 subunit of the WASH complex and the RidL protein from legionella. The intramolecular occlusion of the equivalent binding site in VPS29 when assembled in the Retriever complex prevents Retriever from binding to any of these proteins through these specific mechanisms.

Article Snippet: Primary antibodies: β-Actin (Sigma-Aldrich, A1978; 1:5000 WB, 1:1000 IF), GAPDH (Sigma-Aldrich, G9545; 1:5000 WB), GAPDH (Sigma-Aldrich, G8795; 1:5000 WB), EEA1 (Cell Signalling; 3288S; 1:200 IF), GFP (Roche; 11814460001; clones 7.1/13.1; 1:1000 WB), mCherry/RFP (Abcam, 167453; 1:1000 WB), FLAG-M2 (Sigma, F1804; 1:1000 WB, 1:200 IF), GLUT1 (Abcam; ab115730; 1:1000 WB; 1:400 IF), LAMP1 (Developmental Studies Hybridoma Bank; AB_2296838; clone H4A3; 1:400 IF), VPS29 (Santa Cruz; D-1; sc-398874; 1:500 WB), VPS35 (Abcam, ab97545; 1:1000 WB, 1:400 IF), VPS35 ( Antibodies.com , A83699; 1:400 IF), VPS26 (Abcam, ab23892; 1:1000 WB), VPS35L (Abcam, ab97889; 1:1000 WB), VPS26C (Sigma-Aldrich, ABN87; 1:1000 WB), VPS35L (Invitrogen, PA5-28553; 1:200 IF), SNX1 (BD Transduction Lab, 611482; 1:1000 WB, 1:200 IF), SNX1 (Proteintech, 10304-1-AP; 1:200 IF), SNX2 (BD Transduction Lab, 611308; 1:1000 WB), SNX5 (Abcam, ab180520; 1:1000 WB), SNX6 (Santa Cruz, sc-365965; 1:1000 WB), SNX17 (Proteintech, 10275-1-AP; 1:1000 WB), SNX17 (Sigma, HPA043867, 1:100 IF), SNX27 (Proteintech, 16329-1-AP; 1:1000 WB), SNX27 (Abcam, ab77799; 1:100 IF), HRS/HGS (Enzo Life Sciences, ALX-804-382-C050; 1:2000 WB, 1:100 IF), STAM (Proteintech, 12434-1-AP; 1:2000 WB, 1:100 IF), FAM21 (Gift from Dan Billadeau; 1:2000 WB), Integrin-α5 (Abcam, ab150361; 1:1000 WB, 1;200 IF), DENND4C (Sigma-Aldrich, HPA014917, 1:1000 WB, 1:500 IF), DENND4C (StressMarq Bioscience, SMC-610, 1:100 IF), DENND4A (Abcam, ab117758, 1:500 WB), HAUS2 (ThermoFisher, PA5-31258; 1:500 WB), HAUS6 (Proteintech, 16933-1-AP; 1:1000 WB), HAUS8 (Abcam, ab95970; 1:250 WB), CAV1 (Proteintech, 16447-1-AP; 1:1000 WB), CAVIN1 (Proteintech, 18892-1-AP; 1:1000 WB), TBC1D13 (ThermoFisher, PA5-61110; 1:2000 WB, 1:200 IF), ARHGAP1 (Proteintech, 11169-1-AP; 1:1000 WB, 1:100 IF), VAMP3 (Proteintech, 10702-1-AP; 1:1000 WB, 1:200 IF), NF1 (Proteintech, 27249-1-AP, 1:1000 WB), ARFGEF1 (Abcam, A44423,1:1000 WB), TBC1D4 (Proteintech, 68063), KIDINS220 (Proteintech, 21856-1-AP, 1:1000 WB), ATP7A (Santa Cruz, sc-376467, 1:1000 WB), CTR1 (Abcam, ab129067, 1:1000 WB), LAT1 (Cell Signaling, 5347s, 1:1000 WB), TBC1D5 (Abcam, 203896, 1:1000 WB), VARP/ANKRD27 (Proteintech, 24034-1-AP, 1:1000 WB), RAB10 (Abcam, ab237703, 1:1000 WB, 1:200 IF).

Techniques: Binding Assay, Immunoprecipitation, Co-Immunoprecipitation Assay, Transfection, Expressing, Mutagenesis, Quantitation Assay

(A-G) Predicted alignment error (PAE) plots and pLDDT structural representation for all seven AlphaFold2 predictions of VPS35:VPS29 association with (A) TBC1D1, (B) TBC1D4, (C) TBC1D5, (D) TBC1D13, (E) DENND4A, (F) DENND4C, and (G) DENND11. (H) GFP based co-immunoprecipitation (co-IP) of GFP-VPS29 wild-type (WT) and hydrophobic pocket mutants after transient transfection in HEK293T cells. Here we blotted for TBC1D4, which contrary to DENND4A/C or TBC1D13 show weak interaction under GFP-VPS29 co-IP.

Journal: bioRxiv

Article Title: Mapping the endosomal proximity proteome reveals Retromer as a hub for RAB GTPase regulation

doi: 10.1101/2024.11.22.622898

Figure Lengend Snippet: (A-G) Predicted alignment error (PAE) plots and pLDDT structural representation for all seven AlphaFold2 predictions of VPS35:VPS29 association with (A) TBC1D1, (B) TBC1D4, (C) TBC1D5, (D) TBC1D13, (E) DENND4A, (F) DENND4C, and (G) DENND11. (H) GFP based co-immunoprecipitation (co-IP) of GFP-VPS29 wild-type (WT) and hydrophobic pocket mutants after transient transfection in HEK293T cells. Here we blotted for TBC1D4, which contrary to DENND4A/C or TBC1D13 show weak interaction under GFP-VPS29 co-IP.

Article Snippet: Primary antibodies: β-Actin (Sigma-Aldrich, A1978; 1:5000 WB, 1:1000 IF), GAPDH (Sigma-Aldrich, G9545; 1:5000 WB), GAPDH (Sigma-Aldrich, G8795; 1:5000 WB), EEA1 (Cell Signalling; 3288S; 1:200 IF), GFP (Roche; 11814460001; clones 7.1/13.1; 1:1000 WB), mCherry/RFP (Abcam, 167453; 1:1000 WB), FLAG-M2 (Sigma, F1804; 1:1000 WB, 1:200 IF), GLUT1 (Abcam; ab115730; 1:1000 WB; 1:400 IF), LAMP1 (Developmental Studies Hybridoma Bank; AB_2296838; clone H4A3; 1:400 IF), VPS29 (Santa Cruz; D-1; sc-398874; 1:500 WB), VPS35 (Abcam, ab97545; 1:1000 WB, 1:400 IF), VPS35 ( Antibodies.com , A83699; 1:400 IF), VPS26 (Abcam, ab23892; 1:1000 WB), VPS35L (Abcam, ab97889; 1:1000 WB), VPS26C (Sigma-Aldrich, ABN87; 1:1000 WB), VPS35L (Invitrogen, PA5-28553; 1:200 IF), SNX1 (BD Transduction Lab, 611482; 1:1000 WB, 1:200 IF), SNX1 (Proteintech, 10304-1-AP; 1:200 IF), SNX2 (BD Transduction Lab, 611308; 1:1000 WB), SNX5 (Abcam, ab180520; 1:1000 WB), SNX6 (Santa Cruz, sc-365965; 1:1000 WB), SNX17 (Proteintech, 10275-1-AP; 1:1000 WB), SNX17 (Sigma, HPA043867, 1:100 IF), SNX27 (Proteintech, 16329-1-AP; 1:1000 WB), SNX27 (Abcam, ab77799; 1:100 IF), HRS/HGS (Enzo Life Sciences, ALX-804-382-C050; 1:2000 WB, 1:100 IF), STAM (Proteintech, 12434-1-AP; 1:2000 WB, 1:100 IF), FAM21 (Gift from Dan Billadeau; 1:2000 WB), Integrin-α5 (Abcam, ab150361; 1:1000 WB, 1;200 IF), DENND4C (Sigma-Aldrich, HPA014917, 1:1000 WB, 1:500 IF), DENND4C (StressMarq Bioscience, SMC-610, 1:100 IF), DENND4A (Abcam, ab117758, 1:500 WB), HAUS2 (ThermoFisher, PA5-31258; 1:500 WB), HAUS6 (Proteintech, 16933-1-AP; 1:1000 WB), HAUS8 (Abcam, ab95970; 1:250 WB), CAV1 (Proteintech, 16447-1-AP; 1:1000 WB), CAVIN1 (Proteintech, 18892-1-AP; 1:1000 WB), TBC1D13 (ThermoFisher, PA5-61110; 1:2000 WB, 1:200 IF), ARHGAP1 (Proteintech, 11169-1-AP; 1:1000 WB, 1:100 IF), VAMP3 (Proteintech, 10702-1-AP; 1:1000 WB, 1:200 IF), NF1 (Proteintech, 27249-1-AP, 1:1000 WB), ARFGEF1 (Abcam, A44423,1:1000 WB), TBC1D4 (Proteintech, 68063), KIDINS220 (Proteintech, 21856-1-AP, 1:1000 WB), ATP7A (Santa Cruz, sc-376467, 1:1000 WB), CTR1 (Abcam, ab129067, 1:1000 WB), LAT1 (Cell Signaling, 5347s, 1:1000 WB), TBC1D5 (Abcam, 203896, 1:1000 WB), VARP/ANKRD27 (Proteintech, 24034-1-AP, 1:1000 WB), RAB10 (Abcam, ab237703, 1:1000 WB, 1:200 IF).

Techniques: Immunoprecipitation, Co-Immunoprecipitation Assay, Transfection

(A) Confidence level predictor of homo- and heterodimer formation with a network of Retromer binding TBC and DENND proteins. (B) First three ranked PAE plots of the predicted formation of a TBC1D5 homodimer through carboxy-terminal coiled-coil interactions. (C) First three ranked PAE plots of the predicted formation of TBC1D1 homodimer, TBC1D4 homodimer, full length TBC1D1 and TBC1D4 heterodimer, and heterodimer of the carboxy-terminal regions of TBC1D1 and TBC1D4. (D) pLDDT levels depicted on the predicted AlphaFold model of the coiled-coil carboxy-terminal TBC1D1 and TBC1D4 heterodimer.

Journal: bioRxiv

Article Title: Mapping the endosomal proximity proteome reveals Retromer as a hub for RAB GTPase regulation

doi: 10.1101/2024.11.22.622898

Figure Lengend Snippet: (A) Confidence level predictor of homo- and heterodimer formation with a network of Retromer binding TBC and DENND proteins. (B) First three ranked PAE plots of the predicted formation of a TBC1D5 homodimer through carboxy-terminal coiled-coil interactions. (C) First three ranked PAE plots of the predicted formation of TBC1D1 homodimer, TBC1D4 homodimer, full length TBC1D1 and TBC1D4 heterodimer, and heterodimer of the carboxy-terminal regions of TBC1D1 and TBC1D4. (D) pLDDT levels depicted on the predicted AlphaFold model of the coiled-coil carboxy-terminal TBC1D1 and TBC1D4 heterodimer.

Article Snippet: Primary antibodies: β-Actin (Sigma-Aldrich, A1978; 1:5000 WB, 1:1000 IF), GAPDH (Sigma-Aldrich, G9545; 1:5000 WB), GAPDH (Sigma-Aldrich, G8795; 1:5000 WB), EEA1 (Cell Signalling; 3288S; 1:200 IF), GFP (Roche; 11814460001; clones 7.1/13.1; 1:1000 WB), mCherry/RFP (Abcam, 167453; 1:1000 WB), FLAG-M2 (Sigma, F1804; 1:1000 WB, 1:200 IF), GLUT1 (Abcam; ab115730; 1:1000 WB; 1:400 IF), LAMP1 (Developmental Studies Hybridoma Bank; AB_2296838; clone H4A3; 1:400 IF), VPS29 (Santa Cruz; D-1; sc-398874; 1:500 WB), VPS35 (Abcam, ab97545; 1:1000 WB, 1:400 IF), VPS35 ( Antibodies.com , A83699; 1:400 IF), VPS26 (Abcam, ab23892; 1:1000 WB), VPS35L (Abcam, ab97889; 1:1000 WB), VPS26C (Sigma-Aldrich, ABN87; 1:1000 WB), VPS35L (Invitrogen, PA5-28553; 1:200 IF), SNX1 (BD Transduction Lab, 611482; 1:1000 WB, 1:200 IF), SNX1 (Proteintech, 10304-1-AP; 1:200 IF), SNX2 (BD Transduction Lab, 611308; 1:1000 WB), SNX5 (Abcam, ab180520; 1:1000 WB), SNX6 (Santa Cruz, sc-365965; 1:1000 WB), SNX17 (Proteintech, 10275-1-AP; 1:1000 WB), SNX17 (Sigma, HPA043867, 1:100 IF), SNX27 (Proteintech, 16329-1-AP; 1:1000 WB), SNX27 (Abcam, ab77799; 1:100 IF), HRS/HGS (Enzo Life Sciences, ALX-804-382-C050; 1:2000 WB, 1:100 IF), STAM (Proteintech, 12434-1-AP; 1:2000 WB, 1:100 IF), FAM21 (Gift from Dan Billadeau; 1:2000 WB), Integrin-α5 (Abcam, ab150361; 1:1000 WB, 1;200 IF), DENND4C (Sigma-Aldrich, HPA014917, 1:1000 WB, 1:500 IF), DENND4C (StressMarq Bioscience, SMC-610, 1:100 IF), DENND4A (Abcam, ab117758, 1:500 WB), HAUS2 (ThermoFisher, PA5-31258; 1:500 WB), HAUS6 (Proteintech, 16933-1-AP; 1:1000 WB), HAUS8 (Abcam, ab95970; 1:250 WB), CAV1 (Proteintech, 16447-1-AP; 1:1000 WB), CAVIN1 (Proteintech, 18892-1-AP; 1:1000 WB), TBC1D13 (ThermoFisher, PA5-61110; 1:2000 WB, 1:200 IF), ARHGAP1 (Proteintech, 11169-1-AP; 1:1000 WB, 1:100 IF), VAMP3 (Proteintech, 10702-1-AP; 1:1000 WB, 1:200 IF), NF1 (Proteintech, 27249-1-AP, 1:1000 WB), ARFGEF1 (Abcam, A44423,1:1000 WB), TBC1D4 (Proteintech, 68063), KIDINS220 (Proteintech, 21856-1-AP, 1:1000 WB), ATP7A (Santa Cruz, sc-376467, 1:1000 WB), CTR1 (Abcam, ab129067, 1:1000 WB), LAT1 (Cell Signaling, 5347s, 1:1000 WB), TBC1D5 (Abcam, 203896, 1:1000 WB), VARP/ANKRD27 (Proteintech, 24034-1-AP, 1:1000 WB), RAB10 (Abcam, ab237703, 1:1000 WB, 1:200 IF).

Techniques: Binding Assay