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ATAD3B ATPase family AAA domain containing 3B [ Homo sapiens (human) ]

Gene ID: 83858, updated on 3-Apr-2024

Summary

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Official Symbol
ATAD3Bprovided by HGNC
Official Full Name
ATPase family AAA domain containing 3Bprovided by HGNC
Primary source
HGNC:HGNC:24007
See related
Ensembl:ENSG00000160072 MIM:612317; AllianceGenome:HGNC:24007
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TOB3; AAA-TOB3
Summary
The protein encoded by this gene is localized to the mitochondrial inner membrane, where it can bind to a highly-related protein, ATAD3A. ATAD3A appears to interact with matrix nucleoid complexes, and the encoded protein negatively regulates that interaction. This gene is expressed almost exclusively in pluripotent embryonic stem cells and some cancer cells. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
Expression
Ubiquitous expression in bone marrow (RPKM 7.4), testis (RPKM 6.3) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
1p36.33
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1471765..1509466)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (906136..943970)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1407145..1433228)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr1:1370998-1371187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20 Neighboring gene von Willebrand factor A domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1389959-1390458 Neighboring gene ATPase family AAA domain containing 3C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1397006-1397780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 75 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1409130-1409976 Neighboring gene MPRA-validated peak11 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1443749-1444392 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1444393-1445034 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 76 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 77 Neighboring gene ATPase family AAA domain containing 3A Neighboring gene Sharpr-MPRA regulatory region 185 Neighboring gene transmembrane protein 240

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. ATAD3B is a mitophagy receptor mediating clearance of oxidative stress-induced damaged mitochondrial DNA. Shu L, et al. EMBO J, 2021 Apr 15. PMID 33665835, Free PMC Article
  2. Increased AAA-TOB3 correlates with lymph node metastasis and advanced stage of lung adenocarcinoma. Liu Y, et al. Int J Biol Markers, 2017 Jul 24. PMID 28623644
  3. Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer. Ovaska K, et al. PLoS Comput Biol, 2013. PMID 23818839, Free PMC Article
  4. ATAD3B and SKIL polymorphisms associated with antipsychotic-induced QTc interval change in patients with schizophrenia: a genome-wide association study. Lu Z, et al. Transl Psychiatry, 2022 Feb 8. PMID 35136033, Free PMC Article
  5. ATAD 3A and ATAD 3B are distal 1p-located genes differentially expressed in human glioma cell lines and present in vitro anti-oncogenic and chemoresistant properties. Hubstenberger A, et al. Exp Cell Res, 2008 Sep 10. PMID 18639545

See all (124) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circ_ATAD3B inhibits cell proliferation of breast cancer via mediating the miR-570-3p/MX2 axis.
    Title: Circ_ATAD3B inhibits cell proliferation of breast cancer via mediating the miR-570-3p/MX2 axis.
  2. ATAD3B and SKIL polymorphisms associated with antipsychotic-induced QTc interval change in patients with schizophrenia: a genome-wide association study.
    Title: ATAD3B and SKIL polymorphisms associated with antipsychotic-induced QTc interval change in patients with schizophrenia: a genome-wide association study.
  3. ATAD3B is a mitophagy receptor mediating clearance of oxidative stress-induced damaged mitochondrial DNA.
    Title: ATAD3B is a mitophagy receptor mediating clearance of oxidative stress-induced damaged mitochondrial DNA.
  4. AAA-TOB3 was highly expressed in lung adenocarcinoma, and the up-regulation of AAA-TOB3 correlated with lymph node metastasis and advanced stage of lung adenocarcinoma.
    Title: Increased AAA-TOB3 correlates with lymph node metastasis and advanced stage of lung adenocarcinoma.
  5. ATAD3B region deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism.
    Title: ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism.
  6. exploring ATAD3 mRNA expression, we confirmed the existence of an alternative splicing in rodent and of several mRNA isoforms in human
    Title: Expression analysis of ATAD3 isoforms in rodent and human cell lines and tissues.
  7. results indicated the ATAD3B gene, which does not have ERalpha binding site within 20 kb of its TSS, to be significantly associated with poor patient survival.
    Title: Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer.
  8. ATAD3B is a negative regulator of ATAD3A and may function as an adaptor of mitochondrial homeostasis and metabolism in human pluripotent embryonic stem cells and cancer cells.
    Title: ATAD3B is a human embryonic stem cell specific mitochondrial protein, re-expressed in cancer cells, that functions as dominant negative for the ubiquitous ATAD3A.
  9. ATAD3 may therefore be implicated in an unknown but essential and growth-linked mitochondrial function existing since pluri-cellular -organization and involved in tumorigenesis.
    Title: [ATAD3, a vital membrane-bound mitochondrial ATPase involved in tumor progression].
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vpu vpu HIV-1 Vpu is identified to have a physical interaction with ATPase family, AAA domain containing 3B (ATAD3B) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1273

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in mitochondrion organization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in ficolin-1-rich granule membrane TAS
Traceable Author Statement
more info
  
located_in mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in secretory granule membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
ATPase family AAA domain-containing protein 3B
Names
AAA-ATPase TOB3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001317238.2 → NP_001304167.1  ATPase family AAA domain-containing protein 3B isoform AAA-TOB3s precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (AAA-TOB3s) has a shorter and distinct N-terminus compared to isoform AAA-TOB3l.
    Source sequence(s)
    AL157945, AL645728, BC009938
    UniProtKB/TrEMBL
    Q96T67
    Related
    ENST00000472194.6
    Conserved Domains (2) summary
    pfam00004
    Location:302 → 429
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam12037
    Location:49 → 240
    DUF3523; Domain of unknown function (DUF3523)

  2. NM_031921.6 → NP_114127.3  ATPase family AAA domain-containing protein 3B isoform AAA-TOB3l

    See identical proteins and their annotated locations for NP_114127.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (AAA-TOB3l).
    Source sequence(s)
    AK290586, AL645728, BC009938
    Consensus CDS
    CCDS30.1
    UniProtKB/Swiss-Prot
    A8K3H1, Q5T9A4, Q6ZRB5, Q9BUK4, Q9ULE7
    UniProtKB/TrEMBL
    Q96T67
    Related
    ENSP00000500094.1, ENST00000673477.1
    Conserved Domains (5) summary
    TIGR01242
    Location:198 → 556
    26Sp45; 26S proteasome subunit P45 family
    pfam00004
    Location:348 → 475
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam12037
    Location:42 → 286
    DUF3523; Domain of unknown function (DUF3523)
    cd16269
    Location:151 → 162
    GBP_C; coiled coil [structural motif]
    cl20817
    Location:94 → 179
    GBP_C; Guanylate-binding protein, C-terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    1471765..1509466
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005244806.4 → XP_005244863.1  ATPase family AAA domain-containing protein 3B isoform X1

    UniProtKB/TrEMBL
    Q96T67
    Conserved Domains (3) summary
    TIGR01242
    Location:198 → 564
    26Sp45; 26S proteasome subunit P45 family
    pfam00004
    Location:348 → 475
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam12037
    Location:42 → 286
    DUF3523; Domain of unknown function (DUF3523)

  2. XM_011542244.2 → XP_011540546.1  ATPase family AAA domain-containing protein 3B isoform X6

    UniProtKB/TrEMBL
    Q96T67
    Conserved Domains (5) summary
    TIGR01242
    Location:246 → 604
    26Sp45; 26S proteasome subunit P45 family
    pfam00004
    Location:396 → 523
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam12037
    Location:42 → 334
    DUF3523; Domain of unknown function (DUF3523)
    cd16269
    Location:199 → 210
    GBP_C; coiled coil [structural motif]
    cl20817
    Location:142 → 227
    GBP_C; Guanylate-binding protein, C-terminal domain

  3. XM_047431596.1 → XP_047287552.1  ATPase family AAA domain-containing protein 3B isoform X4

  4. XM_047431583.1 → XP_047287539.1  ATPase family AAA domain-containing protein 3B isoform X2

  5. XM_047431588.1 → XP_047287544.1  ATPase family AAA domain-containing protein 3B isoform X2

  6. XM_011542241.4 → XP_011540543.1  ATPase family AAA domain-containing protein 3B isoform X2

    See identical proteins and their annotated locations for XP_011540543.1

    Conserved Domains (4) summary
    pfam00004
    Location:348 → 450
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam12037
    Location:42 → 286
    DUF3523; Domain of unknown function (DUF3523)
    cd16269
    Location:151 → 162
    GBP_C; coiled coil [structural motif]
    cl20817
    Location:94 → 179
    GBP_C; Guanylate-binding protein, C-terminal domain

  7. XM_047431599.1 → XP_047287555.1  ATPase family AAA domain-containing protein 3B isoform X5

  8. XM_047431593.1 → XP_047287549.1  ATPase family AAA domain-containing protein 3B isoform X3

    UniProtKB/TrEMBL
    Q9H834

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    906136..943970
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338998.1 → XP_054194973.1  ATPase family AAA domain-containing protein 3B isoform X1

  2. XM_054339005.1 → XP_054194980.1  ATPase family AAA domain-containing protein 3B isoform X6

  3. XM_054339003.1 → XP_054194978.1  ATPase family AAA domain-containing protein 3B isoform X4

  4. XM_054338999.1 → XP_054194974.1  ATPase family AAA domain-containing protein 3B isoform X2

  5. XM_054339001.1 → XP_054194976.1  ATPase family AAA domain-containing protein 3B isoform X2

  6. XM_054339000.1 → XP_054194975.1  ATPase family AAA domain-containing protein 3B isoform X2

  7. XM_054339004.1 → XP_054194979.1  ATPase family AAA domain-containing protein 3B isoform X5

  8. XM_054338997.1 → XP_054194972.1  ATPase family AAA domain-containing protein 3B isoform X7

  9. XM_054339002.1 → XP_054194977.1  ATPase family AAA domain-containing protein 3B isoform X3

    UniProtKB/TrEMBL
    Q9H834
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5T9A4.1 GenPept UniProtKB/Swiss-Prot:Q5T9A4

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