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Proteintech ube2d3

Copper metabolism related genes DLD and <t>UBE2D3</t> act as protective factors in KIRC. (A) The OS Kaplan-Meier curve of DLD genes. (B) The ROC curve of DLD gene. (C) The Kaplan-Meier curve (OS) of UBE2D3 gene. The ROC curve of UBE2D3 gene (D) shows the differential expression of UBE2D3 gene at different T stages (E). (F) The expression differences of gene UBE2D3 in different G stages. (G) The calibration curve of the Norman plot is used to predict 1-, 3-, and 5-year survival rates. (H) By drawing a line graph, we predicted the OS period over a time range of 1-, 3-, and 5-year. Each risk factor corresponds to a point axis by drawing a line on the graph. *, P<0.05; **, P<0.01; ***, P<0.001. AUC, area under the curve; CI, confidence interval; G, grade; H, high; HR, hazard ratio; KIRC, kidney renal clear cell carcinoma; L, low; OS, overall survival; ROC, receiver operating characteristic; T, tumor.

Ube2d3, supplied by Proteintech, used in various techniques. Bioz Stars score: 93/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 93 stars, based on 20 article reviews

ube2d3 - by Bioz Stars, 2026-04

93/100 stars

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1) Product Images from "Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma"

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

Journal: Translational Andrology and Urology

doi: 10.21037/tau-2025-427

Copper metabolism related genes DLD and UBE2D3 act as protective factors in KIRC. (A) The OS Kaplan-Meier curve of DLD genes. (B) The ROC curve of DLD gene. (C) The Kaplan-Meier curve (OS) of UBE2D3 gene. The ROC curve of UBE2D3 gene (D) shows the differential expression of UBE2D3 gene at different T stages (E). (F) The expression differences of gene UBE2D3 in different G stages. (G) The calibration curve of the Norman plot is used to predict 1-, 3-, and 5-year survival rates. (H) By drawing a line graph, we predicted the OS period over a time range of 1-, 3-, and 5-year. Each risk factor corresponds to a point axis by drawing a line on the graph. *, P<0.05; **, P<0.01; ***, P<0.001. AUC, area under the curve; CI, confidence interval; G, grade; H, high; HR, hazard ratio; KIRC, kidney renal clear cell carcinoma; L, low; OS, overall survival; ROC, receiver operating characteristic; T, tumor.

Figure Legend Snippet: Copper metabolism related genes DLD and UBE2D3 act as protective factors in KIRC. (A) The OS Kaplan-Meier curve of DLD genes. (B) The ROC curve of DLD gene. (C) The Kaplan-Meier curve (OS) of UBE2D3 gene. The ROC curve of UBE2D3 gene (D) shows the differential expression of UBE2D3 gene at different T stages (E). (F) The expression differences of gene UBE2D3 in different G stages. (G) The calibration curve of the Norman plot is used to predict 1-, 3-, and 5-year survival rates. (H) By drawing a line graph, we predicted the OS period over a time range of 1-, 3-, and 5-year. Each risk factor corresponds to a point axis by drawing a line on the graph. *, P<0.05; **, P<0.01; ***, P<0.001. AUC, area under the curve; CI, confidence interval; G, grade; H, high; HR, hazard ratio; KIRC, kidney renal clear cell carcinoma; L, low; OS, overall survival; ROC, receiver operating characteristic; T, tumor.

Techniques Used: Quantitative Proteomics, Expressing

UBE2D3 functional analysis. (A) UBE2D3 gene expression risk prognostic model. (B) UBE2D3 protein interaction network diagram. (C) Volcano plot based on UBE2D3. (D) GO analysis of differential genes between high and low UBE2D3 groups. (E) KEGG enrichment analysis between high and low UBE2D3 groups. (F) GSEA signal pathway enrichment analysis based on UBE2D3 expression. BP, biological process; CC, cellular component; ES, Enrichment Score; GO, Gene Ontology; GSEA, Gene Set Enrichment Analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular function; NP, nominal P value.

Figure Legend Snippet: UBE2D3 functional analysis. (A) UBE2D3 gene expression risk prognostic model. (B) UBE2D3 protein interaction network diagram. (C) Volcano plot based on UBE2D3. (D) GO analysis of differential genes between high and low UBE2D3 groups. (E) KEGG enrichment analysis between high and low UBE2D3 groups. (F) GSEA signal pathway enrichment analysis based on UBE2D3 expression. BP, biological process; CC, cellular component; ES, Enrichment Score; GO, Gene Ontology; GSEA, Gene Set Enrichment Analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular function; NP, nominal P value.

Techniques Used: Functional Assay, Gene Expression, Expressing

Correlation analysis between UBE2D3 expression and immune cells. (A) Using CIBERSORT method to explore the differences in expression levels of 22 immune cells at different levels of UBE2D3. (B) Correlation analysis between 22 different immune cells. (C) Correlation analysis between UBE2D3 expression levels and biological markers between B cell, Th cell, CD8 + T cell, and DC. (D) Correlation analysis between UBE2D3 expression levels and biological markers between M2 macrophages. (E) Correlation analysis between UBE2D3 expression levels and biological markers between CAF, MDSC, and TAM. (F) Expression of UBE2D3 Correlation analysis chart between levels and biological markers of T exhausted cell, Treg T cell, and macrophages. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001. CAF, cancer-associated fibroblast; CIBERSORT, Cell-Identification By Estimating Relative Subsets Of RNA Transcripts; MDSC, myeloid-derived suppressor cells; TAM, tumor-associated macrophages.

Figure Legend Snippet: Correlation analysis between UBE2D3 expression and immune cells. (A) Using CIBERSORT method to explore the differences in expression levels of 22 immune cells at different levels of UBE2D3. (B) Correlation analysis between 22 different immune cells. (C) Correlation analysis between UBE2D3 expression levels and biological markers between B cell, Th cell, CD8 + T cell, and DC. (D) Correlation analysis between UBE2D3 expression levels and biological markers between M2 macrophages. (E) Correlation analysis between UBE2D3 expression levels and biological markers between CAF, MDSC, and TAM. (F) Expression of UBE2D3 Correlation analysis chart between levels and biological markers of T exhausted cell, Treg T cell, and macrophages. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001. CAF, cancer-associated fibroblast; CIBERSORT, Cell-Identification By Estimating Relative Subsets Of RNA Transcripts; MDSC, myeloid-derived suppressor cells; TAM, tumor-associated macrophages.

Techniques Used: Expressing, Derivative Assay

UBE2D3 affects the tumor immune microenvironment. (A) Using TIMER database to evaluate the correlation between UBE2D3 and immune cells. (B) Box plot shows the distribution of each immune subgroup in KIRC at each copy number state, comparing the infiltration levels of each SCNA category with normal levels. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001. KIRC, kidney renal clear cell carcinoma; SCNA, Somatic Copy-number Alteration; TCGA, The Cancer Genome Atlas; TIMER, Tumor Immune Estimation Resource.

Figure Legend Snippet: UBE2D3 affects the tumor immune microenvironment. (A) Using TIMER database to evaluate the correlation between UBE2D3 and immune cells. (B) Box plot shows the distribution of each immune subgroup in KIRC at each copy number state, comparing the infiltration levels of each SCNA category with normal levels. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001. KIRC, kidney renal clear cell carcinoma; SCNA, Somatic Copy-number Alteration; TCGA, The Cancer Genome Atlas; TIMER, Tumor Immune Estimation Resource.

Techniques Used:

Expression and infiltration of UBE2D3 among different cell populations in the single-cell sequencing dataset. (A) The expression of UBE2D3 in different cells in different datasets. (B) The distribution of GSE139555 cells in the scRNA seq dataset. (C) The distribution of 11 annotation groups in the scRNA seq dataset. (D) The distribution of UBE2D3 in different cells in the scRNA seq dataset. (E) The expression differences of UBE2D3 in different cells between KIRC patients and normal individuals. (F) The expression differences of UBE2D3 in different tumor stages and cells. GSE, GEO Series Accession Number; KIRC, kidney renal clear cell carcinoma; N.S., not significant; NAT, normal adjacent tissue; PBMC, peripheral blood mononuclear cells; scRNA seq, single-cell RNA sequencing; TNM, tumor-node-metastasis; TPM, transcripts per million.

Figure Legend Snippet: Expression and infiltration of UBE2D3 among different cell populations in the single-cell sequencing dataset. (A) The expression of UBE2D3 in different cells in different datasets. (B) The distribution of GSE139555 cells in the scRNA seq dataset. (C) The distribution of 11 annotation groups in the scRNA seq dataset. (D) The distribution of UBE2D3 in different cells in the scRNA seq dataset. (E) The expression differences of UBE2D3 in different cells between KIRC patients and normal individuals. (F) The expression differences of UBE2D3 in different tumor stages and cells. GSE, GEO Series Accession Number; KIRC, kidney renal clear cell carcinoma; N.S., not significant; NAT, normal adjacent tissue; PBMC, peripheral blood mononuclear cells; scRNA seq, single-cell RNA sequencing; TNM, tumor-node-metastasis; TPM, transcripts per million.

Techniques Used: Expressing, Single Cell, Sequencing, RNA Sequencing

UBE2D3 mutation and methylation analysis. (A) Methylation level analysis of UBE2D3 between tumor and normal groups. (B) Methylation level analysis of UBE2D3 in normal group and different stage. (C) Methylation level analysis of UBE2D3 in normal group and different grade stages. (D) Methylation level analysis of UBE2D3 in normal group and different N-stage. (E) Heat map analysis of DNA methylation in the MethSurv database. (F) Correlation between CNV and expression level of UBE2D3. (G) Correlation between CNV level of UBE2D3 and survival. *, P<0.05; **, P<0.01; ***, P<0.001. CNV, copy number variation; Cor, correlation; DFI, disease-free interval; DSS, disease-specific survival; FDR, false discovery rate; KIRC, kidney renal clear cell carcinoma; mRNA, messenger RNA; N, node; OS, overall survival; PFS, progression-free survival; RSEM, RNA-seq by expectation-maximization; TCGA, The Cancer Genome Atlas.

Figure Legend Snippet: UBE2D3 mutation and methylation analysis. (A) Methylation level analysis of UBE2D3 between tumor and normal groups. (B) Methylation level analysis of UBE2D3 in normal group and different stage. (C) Methylation level analysis of UBE2D3 in normal group and different grade stages. (D) Methylation level analysis of UBE2D3 in normal group and different N-stage. (E) Heat map analysis of DNA methylation in the MethSurv database. (F) Correlation between CNV and expression level of UBE2D3. (G) Correlation between CNV level of UBE2D3 and survival. *, P<0.05; **, P<0.01; ***, P<0.001. CNV, copy number variation; Cor, correlation; DFI, disease-free interval; DSS, disease-specific survival; FDR, false discovery rate; KIRC, kidney renal clear cell carcinoma; mRNA, messenger RNA; N, node; OS, overall survival; PFS, progression-free survival; RSEM, RNA-seq by expectation-maximization; TCGA, The Cancer Genome Atlas.

Techniques Used: Mutagenesis, Methylation, DNA Methylation Assay, Expressing, RNA Sequencing

Analyze the drug sensitivity of UBE2D3 in KIRC and predict the IC 50 of the drug. (A) Vincristine. (B) Bosutinib. (C) Ambazone. (D) Finefloxacin. (E) Anagrelide. (F) Meclizine. (G) Dabrafenib. (H) Navitoclax. (I) Propranolol. ***, P<0.001. IC 50 , median inhibitory concentration; KIRC, kidney renal clear cell carcinoma.

Figure Legend Snippet: Analyze the drug sensitivity of UBE2D3 in KIRC and predict the IC 50 of the drug. (A) Vincristine. (B) Bosutinib. (C) Ambazone. (D) Finefloxacin. (E) Anagrelide. (F) Meclizine. (G) Dabrafenib. (H) Navitoclax. (I) Propranolol. ***, P<0.001. IC 50 , median inhibitory concentration; KIRC, kidney renal clear cell carcinoma.

Techniques Used: Concentration Assay

Molecular docking patterns of key drugs and core targets. (A) Vincristine binding to P113 isosite. (B) Bosutinib binding to S100 isosite. (C) Ambazone binding to L89 isosite. (D) Finefloxacin binding to P95 isosite. (E) Anagrelide binding to T98 isosite. (F) Meclizine binding to P57 isosite. (G) Dabrafenib binding to K63 isosite. (H) Navitoclax binding to A68 isosite. (I) Propanol binding to E9 isosite. (J) Different small molecule drugs binding to target UBE2D3 Vina score comparison.

Figure Legend Snippet: Molecular docking patterns of key drugs and core targets. (A) Vincristine binding to P113 isosite. (B) Bosutinib binding to S100 isosite. (C) Ambazone binding to L89 isosite. (D) Finefloxacin binding to P95 isosite. (E) Anagrelide binding to T98 isosite. (F) Meclizine binding to P57 isosite. (G) Dabrafenib binding to K63 isosite. (H) Navitoclax binding to A68 isosite. (I) Propanol binding to E9 isosite. (J) Different small molecule drugs binding to target UBE2D3 Vina score comparison.

Techniques Used: Binding Assay, Comparison

Immunostaining image of UBE2D3 . (A) Expression of UBE2D3 in Para cancer (100×). (B) Expression of UBE2D3 in Para cancer (200×). (C) Expression of UBE2D3 in KIRC (100×). (D) Expression of UBE2D3 in KIRC (200×). (E) IHC staining statistics of UBE2D3 in KIRC and adjacent tissues. **, P<0.01. AOD, average optical density; IHC, immunohistochemistry; KIRC, kidney renal clear cell carcinoma.

Figure Legend Snippet: Immunostaining image of UBE2D3 . (A) Expression of UBE2D3 in Para cancer (100×). (B) Expression of UBE2D3 in Para cancer (200×). (C) Expression of UBE2D3 in KIRC (100×). (D) Expression of UBE2D3 in KIRC (200×). (E) IHC staining statistics of UBE2D3 in KIRC and adjacent tissues. **, P<0.01. AOD, average optical density; IHC, immunohistochemistry; KIRC, kidney renal clear cell carcinoma.

Techniques Used: Immunostaining, Expressing, Immunohistochemistry

Image Search Results

A. PP2A subunits PP2A- 3×Flag Aα/ Strep Cα/B55α were expressed as individual proteins, in PP2A subcomplexes PP2A-AC/AB/CB, and as the heterotrimeric PP2A-ACB holoenzyme in insect cells. PP2A extracts were mixed as indicated with 6×His-MBP KBTBD4 extract and affinity purified to test for binding of KBTBD4 to PP2A subunits and subcomplexes. B. Purified PP2A subunits and (sub-)complexes were ubiquitylated in vitro with purified KBTBD4, CUL3 NEDD8 -RBX1, UBE1, UBE2D3 and fluorescently labeled ubiquitin. Representative result of n=2 independent experiments. C. Cellular extracts from HEK293T cells and Δ KBTBD4 cell lines #1and #2 were separated over a 5-20% sucrose gradient by ultracentrifugation. Fractions were probed for indicated proteins by western blot. Representative result of n=2 experiments.

Journal: bioRxiv

Article Title: Medulloblastoma-Associated KBTBD4 Mutations Disrupt PP2A-A Orphan Quality Control

doi: 10.64898/2026.03.02.709011

Figure Lengend Snippet: A. PP2A subunits PP2A- 3×Flag Aα/ Strep Cα/B55α were expressed as individual proteins, in PP2A subcomplexes PP2A-AC/AB/CB, and as the heterotrimeric PP2A-ACB holoenzyme in insect cells. PP2A extracts were mixed as indicated with 6×His-MBP KBTBD4 extract and affinity purified to test for binding of KBTBD4 to PP2A subunits and subcomplexes. B. Purified PP2A subunits and (sub-)complexes were ubiquitylated in vitro with purified KBTBD4, CUL3 NEDD8 -RBX1, UBE1, UBE2D3 and fluorescently labeled ubiquitin. Representative result of n=2 independent experiments. C. Cellular extracts from HEK293T cells and Δ KBTBD4 cell lines #1and #2 were separated over a 5-20% sucrose gradient by ultracentrifugation. Fractions were probed for indicated proteins by western blot. Representative result of n=2 experiments.

Article Snippet: Ubiquitylation assays were carried out in 20 μL reactions with final concentrations of 1 μM PP2A (PP2A-A or in indicated complex), 0.1 μM UBE1 (R&D Systems, E-304), 0.2 μM UBE2D3 (R&D Systems, E2-627), 0.5 μM KBTBD4, 0.4 μM CUL3 NEDD8 -RBX1 (CRL), 7.5 μM ubiquitin IRdye680 (gift from Jake Aguirre, as published in ( )), 5 mM ATP, 2.5 mM MgCl 2 , in a buffer of 20 mM HEPES pH 7.4, 150 mM NaCl and 1 mM DTT.

Techniques: Affinity Purification, Binding Assay, Purification, In Vitro, Labeling, Ubiquitin Proteomics, Western Blot

A. Flag purification of transiently expressed wild-type KBTBD4 3×Flag and medulloblastoma hotspot mutants to probe for binding to 2×HA PP2A-A. B. PP2A-A stability was monitored by flow cytometry through transient expression of the dual fluorescence reporter in HEK293T cells and Δ KBTBD4 #1 with co-expression of KBTBD4 WT or the MB mutant KBTBD4 PR construct. C. Quantification of the stability of PP2A-A as monitored by flow cytometry after expression of the dual fluorescence reporter and indicated KBTBD4 constructs (WT, MB mutant PR, CUL3-binding mutant C3). Data was measured at least in triplicates, and the median fluorescence signal ratio of GFP over mCherry was normalized to HEK293T control. D. Ubiquitin conjugates were purified under denaturing conditions from Δ KBTBD4 #1 cells, virally transduced to rescue with indicated KBTBD4 constructs, and transiently transfected to express His-tagged ubiquitin and myc PP2A-A. E. Purified PP2A-A was ubiquitylated in vitro with purified KBTBD4 (WT and MB cancer mutant PR), CUL3 NEDD8 -RBX1, UBE1, UBE2D3 and fluorescently labeled ubiquitin. Representative result of n=2 independent experiments. F. Flag purification of transiently expressed 3×Flag PP2A-A (wild-type and cancer mutants P179R and R183W) to probe for binding to KBTBD4 3×HA . G. Purified PP2A-A (WT, and cancer mutants P179R and R183W) was ubiquitylated in vitro with purified KBTBD4, CUL3 NEDD8 -RBX1, UBE1, UBE2D3 and fluorescently labeled ubiquitin. Representative result of n=2 independent experiments. H. Quantification of the stability of wild-type PP2A-A and indicated mutants as monitored by flow cytometry after viral transduction of a dual fluorescence reporter. Data representative of n=3 independent experiments.

Journal: bioRxiv

Article Title: Medulloblastoma-Associated KBTBD4 Mutations Disrupt PP2A-A Orphan Quality Control

doi: 10.64898/2026.03.02.709011

Figure Lengend Snippet: A. Flag purification of transiently expressed wild-type KBTBD4 3×Flag and medulloblastoma hotspot mutants to probe for binding to 2×HA PP2A-A. B. PP2A-A stability was monitored by flow cytometry through transient expression of the dual fluorescence reporter in HEK293T cells and Δ KBTBD4 #1 with co-expression of KBTBD4 WT or the MB mutant KBTBD4 PR construct. C. Quantification of the stability of PP2A-A as monitored by flow cytometry after expression of the dual fluorescence reporter and indicated KBTBD4 constructs (WT, MB mutant PR, CUL3-binding mutant C3). Data was measured at least in triplicates, and the median fluorescence signal ratio of GFP over mCherry was normalized to HEK293T control. D. Ubiquitin conjugates were purified under denaturing conditions from Δ KBTBD4 #1 cells, virally transduced to rescue with indicated KBTBD4 constructs, and transiently transfected to express His-tagged ubiquitin and myc PP2A-A. E. Purified PP2A-A was ubiquitylated in vitro with purified KBTBD4 (WT and MB cancer mutant PR), CUL3 NEDD8 -RBX1, UBE1, UBE2D3 and fluorescently labeled ubiquitin. Representative result of n=2 independent experiments. F. Flag purification of transiently expressed 3×Flag PP2A-A (wild-type and cancer mutants P179R and R183W) to probe for binding to KBTBD4 3×HA . G. Purified PP2A-A (WT, and cancer mutants P179R and R183W) was ubiquitylated in vitro with purified KBTBD4, CUL3 NEDD8 -RBX1, UBE1, UBE2D3 and fluorescently labeled ubiquitin. Representative result of n=2 independent experiments. H. Quantification of the stability of wild-type PP2A-A and indicated mutants as monitored by flow cytometry after viral transduction of a dual fluorescence reporter. Data representative of n=3 independent experiments.

Techniques: Purification, Binding Assay, Flow Cytometry, Expressing, Fluorescence, Mutagenesis, Construct, Control, Ubiquitin Proteomics, Transfection, In Vitro, Labeling, Transduction

(A) Schematic of human TRIM32 highlighting domain architecture. The four lysine residues in the coiled-coil domain identified by mass spectrum analysis as autoubiquitination sites in the current study are indicated in red. The hydrophobic helix loop in TRIM32 NHL domain is labeled in blue. (B) Depiction of the core components of the TRIM32 in vitro auto-ubiquitination reconstitution assay including UBE1, the E2 enzyme UBE2D3, ubiquitin, TRIM32, and ATP. (C) Coomassie stained SDS-PAGE gels of in vitro TRIM32 autoubiquitination assays showing that compared with WT TRIM32, the quadruple point mutation TRIM32 4KR (K175R/K182R/K204R/K215R) prevents autoubiquitination. Colored box indicates the band for TRIM32 (cyan) and ubiquitin (blue) level quantification, respectively. Red arrow indicates HWM polyubiquitinated TRIM32 in the loading well. (D) Quantification of time course change in (C) measuring TRIM32 or ubiquitin level via densitometry. Combined data from three independent experiments are shown. Data are presented as mean ± s.e.m. (E) Ubiquitin linkage composition by AQUA MS from in vitro TRIM32 autoubiquitination assays performed in technical duplicate. (F) Coomassie stained SDS-PAGE gel image representing TRIM32 autoubiquitination assays before and after Lb pro * treatment for 1 hours. Released ubiquitin (blue box) was analyzed by MS to identify GG-modified ubiquitin species. (G) TRIM32 assembles branched polyUb, according to intact MS analysis. Quantification by spectra deconvolution of individual ubiquitin species from (F) in autoubiquitination assay.

Journal: bioRxiv

Article Title: TRIM32–UBQLN2–p62 axis promotes TDP-43 inclusion formation and amyloid aggregation through shuttle condensates

doi: 10.64898/2026.02.11.705390

Figure Lengend Snippet: (A) Schematic of human TRIM32 highlighting domain architecture. The four lysine residues in the coiled-coil domain identified by mass spectrum analysis as autoubiquitination sites in the current study are indicated in red. The hydrophobic helix loop in TRIM32 NHL domain is labeled in blue. (B) Depiction of the core components of the TRIM32 in vitro auto-ubiquitination reconstitution assay including UBE1, the E2 enzyme UBE2D3, ubiquitin, TRIM32, and ATP. (C) Coomassie stained SDS-PAGE gels of in vitro TRIM32 autoubiquitination assays showing that compared with WT TRIM32, the quadruple point mutation TRIM32 4KR (K175R/K182R/K204R/K215R) prevents autoubiquitination. Colored box indicates the band for TRIM32 (cyan) and ubiquitin (blue) level quantification, respectively. Red arrow indicates HWM polyubiquitinated TRIM32 in the loading well. (D) Quantification of time course change in (C) measuring TRIM32 or ubiquitin level via densitometry. Combined data from three independent experiments are shown. Data are presented as mean ± s.e.m. (E) Ubiquitin linkage composition by AQUA MS from in vitro TRIM32 autoubiquitination assays performed in technical duplicate. (F) Coomassie stained SDS-PAGE gel image representing TRIM32 autoubiquitination assays before and after Lb pro * treatment for 1 hours. Released ubiquitin (blue box) was analyzed by MS to identify GG-modified ubiquitin species. (G) TRIM32 assembles branched polyUb, according to intact MS analysis. Quantification by spectra deconvolution of individual ubiquitin species from (F) in autoubiquitination assay.

Article Snippet: Bacterial plasmids obtained from Addgene include: UBE1 (Addgene plasmid # 34965), UBE2D3 (Addgene plasmid # 12643), ANXA11 (Addgene plasmid # 164496), p62 (Addgene plasmid # 190929), TDP-43 (Addgene plasmid # 133320 and plasmid # 27462).

Techniques: Labeling, In Vitro, Ubiquitin Proteomics, Reconstitution Assay, Staining, SDS Page, Mutagenesis, Modification

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Copper metabolism related genes DLD and UBE2D3 act as protective factors in KIRC. (A) The OS Kaplan-Meier curve of DLD genes. (B) The ROC curve of DLD gene. (C) The Kaplan-Meier curve (OS) of UBE2D3 gene. The ROC curve of UBE2D3 gene (D) shows the differential expression of UBE2D3 gene at different T stages (E). (F) The expression differences of gene UBE2D3 in different G stages. (G) The calibration curve of the Norman plot is used to predict 1-, 3-, and 5-year survival rates. (H) By drawing a line graph, we predicted the OS period over a time range of 1-, 3-, and 5-year. Each risk factor corresponds to a point axis by drawing a line on the graph. *, P<0.05; **, P<0.01; ***, P<0.001. AUC, area under the curve; CI, confidence interval; G, grade; H, high; HR, hazard ratio; KIRC, kidney renal clear cell carcinoma; L, low; OS, overall survival; ROC, receiver operating characteristic; T, tumor.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques: Quantitative Proteomics, Expressing

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: UBE2D3 functional analysis. (A) UBE2D3 gene expression risk prognostic model. (B) UBE2D3 protein interaction network diagram. (C) Volcano plot based on UBE2D3. (D) GO analysis of differential genes between high and low UBE2D3 groups. (E) KEGG enrichment analysis between high and low UBE2D3 groups. (F) GSEA signal pathway enrichment analysis based on UBE2D3 expression. BP, biological process; CC, cellular component; ES, Enrichment Score; GO, Gene Ontology; GSEA, Gene Set Enrichment Analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular function; NP, nominal P value.

Techniques: Functional Assay, Gene Expression, Expressing

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Correlation analysis between UBE2D3 expression and immune cells. (A) Using CIBERSORT method to explore the differences in expression levels of 22 immune cells at different levels of UBE2D3. (B) Correlation analysis between 22 different immune cells. (C) Correlation analysis between UBE2D3 expression levels and biological markers between B cell, Th cell, CD8 + T cell, and DC. (D) Correlation analysis between UBE2D3 expression levels and biological markers between M2 macrophages. (E) Correlation analysis between UBE2D3 expression levels and biological markers between CAF, MDSC, and TAM. (F) Expression of UBE2D3 Correlation analysis chart between levels and biological markers of T exhausted cell, Treg T cell, and macrophages. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001. CAF, cancer-associated fibroblast; CIBERSORT, Cell-Identification By Estimating Relative Subsets Of RNA Transcripts; MDSC, myeloid-derived suppressor cells; TAM, tumor-associated macrophages.

Techniques: Expressing, Derivative Assay

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: UBE2D3 affects the tumor immune microenvironment. (A) Using TIMER database to evaluate the correlation between UBE2D3 and immune cells. (B) Box plot shows the distribution of each immune subgroup in KIRC at each copy number state, comparing the infiltration levels of each SCNA category with normal levels. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001. KIRC, kidney renal clear cell carcinoma; SCNA, Somatic Copy-number Alteration; TCGA, The Cancer Genome Atlas; TIMER, Tumor Immune Estimation Resource.

Techniques:

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Expression and infiltration of UBE2D3 among different cell populations in the single-cell sequencing dataset. (A) The expression of UBE2D3 in different cells in different datasets. (B) The distribution of GSE139555 cells in the scRNA seq dataset. (C) The distribution of 11 annotation groups in the scRNA seq dataset. (D) The distribution of UBE2D3 in different cells in the scRNA seq dataset. (E) The expression differences of UBE2D3 in different cells between KIRC patients and normal individuals. (F) The expression differences of UBE2D3 in different tumor stages and cells. GSE, GEO Series Accession Number; KIRC, kidney renal clear cell carcinoma; N.S., not significant; NAT, normal adjacent tissue; PBMC, peripheral blood mononuclear cells; scRNA seq, single-cell RNA sequencing; TNM, tumor-node-metastasis; TPM, transcripts per million.

Techniques: Expressing, Single Cell, Sequencing, RNA Sequencing

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: UBE2D3 mutation and methylation analysis. (A) Methylation level analysis of UBE2D3 between tumor and normal groups. (B) Methylation level analysis of UBE2D3 in normal group and different stage. (C) Methylation level analysis of UBE2D3 in normal group and different grade stages. (D) Methylation level analysis of UBE2D3 in normal group and different N-stage. (E) Heat map analysis of DNA methylation in the MethSurv database. (F) Correlation between CNV and expression level of UBE2D3. (G) Correlation between CNV level of UBE2D3 and survival. *, P<0.05; **, P<0.01; ***, P<0.001. CNV, copy number variation; Cor, correlation; DFI, disease-free interval; DSS, disease-specific survival; FDR, false discovery rate; KIRC, kidney renal clear cell carcinoma; mRNA, messenger RNA; N, node; OS, overall survival; PFS, progression-free survival; RSEM, RNA-seq by expectation-maximization; TCGA, The Cancer Genome Atlas.

Techniques: Mutagenesis, Methylation, DNA Methylation Assay, Expressing, RNA Sequencing

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Analyze the drug sensitivity of UBE2D3 in KIRC and predict the IC 50 of the drug. (A) Vincristine. (B) Bosutinib. (C) Ambazone. (D) Finefloxacin. (E) Anagrelide. (F) Meclizine. (G) Dabrafenib. (H) Navitoclax. (I) Propranolol. ***, P<0.001. IC 50 , median inhibitory concentration; KIRC, kidney renal clear cell carcinoma.

Techniques: Concentration Assay

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Molecular docking patterns of key drugs and core targets. (A) Vincristine binding to P113 isosite. (B) Bosutinib binding to S100 isosite. (C) Ambazone binding to L89 isosite. (D) Finefloxacin binding to P95 isosite. (E) Anagrelide binding to T98 isosite. (F) Meclizine binding to P57 isosite. (G) Dabrafenib binding to K63 isosite. (H) Navitoclax binding to A68 isosite. (I) Propanol binding to E9 isosite. (J) Different small molecule drugs binding to target UBE2D3 Vina score comparison.

Techniques: Binding Assay, Comparison

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Immunostaining image of UBE2D3 . (A) Expression of UBE2D3 in Para cancer (100×). (B) Expression of UBE2D3 in Para cancer (200×). (C) Expression of UBE2D3 in KIRC (100×). (D) Expression of UBE2D3 in KIRC (200×). (E) IHC staining statistics of UBE2D3 in KIRC and adjacent tissues. **, P<0.01. AOD, average optical density; IHC, immunohistochemistry; KIRC, kidney renal clear cell carcinoma.

Techniques: Immunostaining, Expressing, Immunohistochemistry

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