Gene description for ATG4B
Gene name autophagy related 4B, cysteine peptidase
Gene symbol ATG4B
Other names/aliases APG4B
AUTL1
Species Homo sapiens
 Database cross references - ATG4B
ExoCarta ExoCarta_23192
Vesiclepedia VP_23192
Entrez Gene 23192
HGNC 20790
MIM 611338
UniProt Q9Y4P1  
 ATG4B identified in sEVs derived from the following tissue/cell type
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Hepatocytes 26054723    
Mesenchymal stem cells 36408942    
 Gene ontology annotations for ATG4B
Molecular Function
    endopeptidase activity GO:0004175 IDA
    cysteine-type endopeptidase activity GO:0004197 IBA
    cysteine-type endopeptidase activity GO:0004197 IDA
    cysteine-type endopeptidase activity GO:0004197 TAS
    protein binding GO:0005515 IPI
    cysteine-type peptidase activity GO:0008234 IDA
    protein-phosphatidylethanolamide deconjugating activity GO:0019786 IBA
    protein-phosphatidylethanolamide deconjugating activity GO:0019786 IDA
    scaffold protein binding GO:0097110 IPI
Biological Process
    autophagosome assembly GO:0000045 IBA
    autophagosome assembly GO:0000045 IDA
    mitophagy GO:0000423 IBA
    mitophagy GO:0000423 IMP
    proteolysis GO:0006508 IDA
    autophagy GO:0006914 IDA
    protein transport GO:0015031 IEA
    macroautophagy GO:0016236 TAS
    microautophagy GO:0016237 IDA
    protein processing GO:0016485 IBA
    otolith mineralization completed early in development GO:0031173 ISS
    protein localization to phagophore assembly site GO:0034497 IMP
    piecemeal microautophagy of the nucleus GO:0034727 IBA
    aggrephagy GO:0035973 IBA
    protein delipidation GO:0051697 IDA
Subcellular Localization
    autophagosome membrane GO:0000421 IDA
    cytoplasm GO:0005737 IBA
    mitochondrion GO:0005739 IEA
    endoplasmic reticulum GO:0005783 IEA
    cytosol GO:0005829 TAS
    cytoplasmic vesicle GO:0031410 IEA
 Experiment description of studies that identified ATG4B in sEVs
1
Experiment ID 489
MISEV standards
✔
EM
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 6
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
2
Experiment ID 490
MISEV standards
✔
EM
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 7
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
3
Experiment ID 491
MISEV standards
✔
EM
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 8
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
4
Experiment ID 492
MISEV standards
✔
EM
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 9
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
5
Experiment ID 237
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|Alix|HSC70|GAPDH
Enriched markers
✔
HSP90B1
Negative markers
✔
qNano
Particle analysis
Identified molecule mRNA
Identification method RNA Sequencing
PubMed ID 26054723    
Organism Homo sapiens
Experiment description Hepatocellular carcinoma-derived exosomes promote motility of immortalized hepatocyte through transfer of oncogenic proteins and RNAs
Authors "He M, Qin H, Poon TC, Sze SC, Ding X, Co NN, Ngai SM, Chan TF, Wong N"
Journal name Carcinogenesis
Publication year 2015
Sample Hepatocytes
Sample name MIHA
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
RNA
Methods used in the study Western blotting
Mass spectrometry
RNA Sequencing
6
Experiment ID 488
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD81|CD63|GAPDH|SDCBP|LAMP1|TFRC|UCHL1|FLOT2|LAMP2|FLOT1|ICAM1|RAB5B|CD151|RAB35|TSG101|RAB5A|CD82
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Homo sapiens
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Mesenchymal stem cells
Sample name UCMSC
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
 Protein-protein interactions for ATG4B
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 GABARAPL1 23710
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Co-crystal Structure Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
2 RAB7B  
Affinity Capture-Western Homo sapiens
3 MAP1LC3C  
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Two-hybrid Homo sapiens
4 GTF2F1 2962
Affinity Capture-MS Homo sapiens
5 KRT4 3851
Affinity Capture-MS Homo sapiens
6 GLUD1 2746
Affinity Capture-MS Homo sapiens
7 EIF3A 8661
Affinity Capture-MS Homo sapiens
8 RPS3A 6189
Affinity Capture-MS Homo sapiens
9 PSMD6 9861
Affinity Capture-MS Homo sapiens
10 EIF2S3 1968
Affinity Capture-MS Homo sapiens
11 RPL30 6156
Affinity Capture-MS Homo sapiens
12 RPL13A 23521
Affinity Capture-MS Homo sapiens
13 RPS19 6223
Affinity Capture-MS Homo sapiens
14 RPL10 6134
Affinity Capture-MS Homo sapiens
15 C9orf78 51759
Affinity Capture-MS Homo sapiens
16 EIF4A1 1973
Affinity Capture-MS Homo sapiens
17 CCDC124 115098
Affinity Capture-MS Homo sapiens
18 RPS3 6188
Affinity Capture-MS Homo sapiens
19 MAP1LC3B 81631
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Two-hybrid Homo sapiens
Biochemical Activity Homo sapiens
20 SRP54 6729
Affinity Capture-MS Homo sapiens
21 TOP2A 7153
Affinity Capture-MS Homo sapiens
22 FANK1  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
23 GTF2F2 2963
Affinity Capture-MS Homo sapiens
24 H1FX 8971
Affinity Capture-MS Homo sapiens
25 EIF3B 8662
Affinity Capture-MS Homo sapiens
26 RPL24 6152
Affinity Capture-MS Homo sapiens
27 RPS8 6202
Affinity Capture-MS Homo sapiens
28 RPS5 6193
Affinity Capture-MS Homo sapiens
29 RPS9 6203
Affinity Capture-MS Homo sapiens
30 ZCCHC3  
Affinity Capture-MS Homo sapiens
31 ATG3 64422
Affinity Capture-MS Homo sapiens
32 SMC2 10592
Affinity Capture-MS Homo sapiens
33 CSNK1D 1453
Affinity Capture-MS Homo sapiens
34 PABPC4 8761
Affinity Capture-MS Homo sapiens
35 RPL19 6143
Affinity Capture-MS Homo sapiens
36 PRNP 5621
Affinity Capture-MS Homo sapiens
37 FAS 355
Proximity Label-MS Homo sapiens
38 YWHAB 7529
Co-fractionation Homo sapiens
39 RPS23 6228
Affinity Capture-MS Homo sapiens
40 RPL27 6155
Affinity Capture-MS Homo sapiens
41 EIF3K 27335
Affinity Capture-MS Homo sapiens
42 USP10 9100
Affinity Capture-MS Homo sapiens
43 RPL9 6133
Affinity Capture-MS Homo sapiens
44 STAU1 6780
Affinity Capture-MS Homo sapiens
45 PABPC1 26986
Affinity Capture-MS Homo sapiens
46 GABARAP 11337
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
47 RPL31 6160
Affinity Capture-MS Homo sapiens
48 DCP1A 55802
Affinity Capture-MS Homo sapiens
49 ULK1  
Affinity Capture-MS Homo sapiens
50 CSNK1E 1454
Affinity Capture-MS Homo sapiens
51 DHX9 1660
Affinity Capture-MS Homo sapiens
52 RPLP0 6175
Affinity Capture-MS Homo sapiens
53 RRP1B 23076
Affinity Capture-MS Homo sapiens
54 RPS15A 6210
Affinity Capture-MS Homo sapiens
55 CAMKK2 10645
Affinity Capture-MS Homo sapiens
56 STAM 8027
Affinity Capture-MS Homo sapiens
57 RPL11 6135
Affinity Capture-MS Homo sapiens
58 BAG3 9531
Affinity Capture-MS Homo sapiens
Affinity Capture-Luminescence Homo sapiens
59 STK3 6788
Affinity Capture-MS Homo sapiens
60 RPL32 6161
Affinity Capture-MS Homo sapiens
61 LINC00341  
Two-hybrid Homo sapiens
62 AMBRA1  
Affinity Capture-MS Homo sapiens
63 DDX3Y 8653
Affinity Capture-MS Homo sapiens
64 SLC27A4 10999
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
65 ANXA1 301
Affinity Capture-MS Homo sapiens
66 ATG12  
Affinity Capture-MS Homo sapiens
67 RPS7 6201
Affinity Capture-MS Homo sapiens
68 RPL3 6122
Affinity Capture-MS Homo sapiens
69 EIF4E 1977
Affinity Capture-MS Homo sapiens
70 NXF1 10482
Affinity Capture-RNA Homo sapiens
71 RPS13 6207
Affinity Capture-MS Homo sapiens
72 RPL22 6146
Affinity Capture-MS Homo sapiens
73 KTN1 3895
Affinity Capture-MS Homo sapiens
74 RPS16 6217
Affinity Capture-MS Homo sapiens
75 EIF3H 8667
Affinity Capture-MS Homo sapiens
76 AIMP1 9255
Affinity Capture-MS Homo sapiens
77 ATG10  
Affinity Capture-MS Homo sapiens
78 COA4  
Affinity Capture-MS Homo sapiens
79 PLEKHA4 57664
Affinity Capture-MS Homo sapiens
80 FBXW11  
Affinity Capture-MS Homo sapiens
81 STK16 8576
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
82 RPS25 6230
Affinity Capture-MS Homo sapiens
83 ILF3 3609
Affinity Capture-MS Homo sapiens
84 RPL6 6128
Affinity Capture-MS Homo sapiens
85 PRRC2C 23215
Affinity Capture-MS Homo sapiens
86 NUFIP2 57532
Affinity Capture-MS Homo sapiens
87 RPS12 6206
Affinity Capture-MS Homo sapiens
88 GABARAPL2 11345
Affinity Capture-MS Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-MS Homo sapiens
89 RPS4X 6191
Affinity Capture-MS Homo sapiens
90 SQSTM1 8878
Affinity Capture-Western Homo sapiens
91 RPS15 6209
Affinity Capture-MS Homo sapiens
92 SHMT2 6472
Affinity Capture-RNA Homo sapiens
93 DDX58 23586
Affinity Capture-RNA Homo sapiens
94 RPL34 6164
Affinity Capture-MS Homo sapiens
95 RPS26 6231
Affinity Capture-MS Homo sapiens
96 NUP50 10762
Affinity Capture-MS Homo sapiens
97 NCAPD2 9918
Affinity Capture-MS Homo sapiens
98 MAP1LC3A 84557
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Two-hybrid Homo sapiens
Co-crystal Structure Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
99 RPL38 6169
Affinity Capture-MS Homo sapiens
100 MOV10 4343
Affinity Capture-RNA Homo sapiens
101 EIF3J 8669
Affinity Capture-MS Homo sapiens
102 RPL23 9349
Affinity Capture-MS Homo sapiens
103 MGME1  
Affinity Capture-MS Homo sapiens
104 KDM5C  
Affinity Capture-MS Homo sapiens
105 RPL28 6158
Affinity Capture-MS Homo sapiens
106 SERBP1 26135
Affinity Capture-MS Homo sapiens
107 PRMT1 3276
Affinity Capture-MS Homo sapiens
108 RPL17 6139
Affinity Capture-MS Homo sapiens
109 MAP1LC3B2  
Affinity Capture-MS Homo sapiens
View the network image/svg+xml
 Pathways in which ATG4B is involved
PathwayEvidenceSource
Autophagy TAS Reactome
Macroautophagy TAS Reactome





Perform bioinformatics analysis of your extracellular vesicle data set using FunRich, a open access standalone tool. NEW UPDATED VERSION OF FunRich available for download (12/09/2016) from here