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AP3D1 adaptor related protein complex 3 subunit delta 1 [ Homo sapiens (human) ]

Gene ID: 8943, updated on 17-Jun-2019

Summary

Official Symbol
AP3D1provided by HGNC
Official Full Name
adaptor related protein complex 3 subunit delta 1provided by HGNC
Primary source
HGNC:HGNC:568
See related
Ensembl:ENSG00000065000 MIM:607246
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
ADTD; HPS10; hBLVR
Summary
The protein encoded by this gene is a subunit of the AP3 adaptor-like complex, which is not clathrin-associated, but is associated with the golgi region, as well as more peripheral structures. The AP-3 complex facilitates the budding of vesicles from the golgi membrane, and may be directly involved in trafficking to lysosomes. This subunit is implicated in intracellular biogenesis and trafficking of pigment granules, and possibly platelet dense granules and neurotransmitter vesicles. Defects in this gene are a cause of a new type of Hermansky-Pudlak syndrome. [provided by RefSeq, Feb 2017]
Expression
Ubiquitous expression in testis (RPKM 31.2), kidney (RPKM 22.6) and 25 other tissues See more
Orthologs

Genomic context

See AP3D1 in Genome Data Viewer
Location:
19p13.3
Exon count:
32
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (2100988..2151620, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2100987..2151556, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene MOB kinase activator 3A Neighboring gene IZUMO family member 4 Neighboring gene DOT1 like histone lysine methyltransferase Neighboring gene pleckstrin homology domain containing J1 Neighboring gene microRNA 1227

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Hermansky-Pudlak syndrome 10
MedGen: C4310746 OMIM: 617050 GeneReviews: Hermansky-Pudlak Syndrome
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 delta 1 subunit (AP3D1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Envelope surface glycoprotein gp160, precursor env In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 delta 1 subunit (AP3D1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 delta 1 subunit (AP3D1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
nef HIV-1 Nef co-localizes with the delta subunit of adaptor protein complex 3 (AP-3) in a juxtanuclear region near the cell center of HeLa cells PubMed
nef The dileucine residues and glutamic acid residue of the EXXXLL motif in HIV-1 Nef (amino acid residues 159-165) are required for Nef binding and stabilization of AP-3 PubMed
Pr55(Gag) gag The matrix region (residues 1-133) of HIV-1 Gag interacts directly with the delta subunit of the AP-3 complex, and this interaction is required for Gag trafficking to multivesicular bodies PubMed
gag Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 delta 1 subunit (AP3D1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
gag In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding PubMed
gag AP3D1 deficiency in HPS2 fibroblasts inhibits HIV-1 Gag assembly and release PubMed
matrix gag NMR analysis shows that HIV-1 Matrix Protein fails to directly interact with AP-3delta PubMed
gag The matrix region of HIV-1 Gag interacts directly with the delta subunit of the AP-3 complex, and this interaction is required for Gag trafficking to multivesicular bodies PubMed
gag In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Lysosome, organism-specific biosystem (from KEGG)
    Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Lysosome, conserved biosystem (from KEGG)
    Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
Golgi to vacuole transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
anterograde axonal transport ISS
Inferred from Sequence or Structural Similarity
more info
 
anterograde synaptic vesicle transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
anterograde synaptic vesicle transport ISS
Inferred from Sequence or Structural Similarity
more info
 
antigen processing and presentation, exogenous lipid antigen via MHC class Ib IEA
Inferred from Electronic Annotation
more info
 
endosome to melanosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
melanosome organization IC
Inferred by Curator
more info
PubMed 
neurotransmitter receptor transport, postsynaptic endosome to lysosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of NK T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
protein localization to membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of sequestering of zinc ion IMP
Inferred from Mutant Phenotype
more info
PubMed 
synaptic vesicle budding from endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synaptic vesicle membrane organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
AP-3 adaptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi apparatus TAS
Traceable Author Statement
more info
PubMed 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
axon cytoplasm IEA
Inferred from Electronic Annotation
more info
 
endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
lysosomal membrane HDA PubMed 
membrane HDA PubMed 
postsynapse IEA
Inferred from Electronic Annotation
more info
 
presynaptic endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
terminal bouton IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
AP-3 complex subunit delta-1
Names
AP-3 complex delta subunit, partial CDS
adapter-related protein complex 3 subunit delta-1
adaptor related protein complex 3 delta 1 subunit
delta adaptin
subunit of putative vesicle coat adaptor complex AP-3

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_052886.2 RefSeqGene

    Range
    17903..68481
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1207

mRNA and Protein(s)

  1. NM_001261826.3NP_001248755.1  AP-3 complex subunit delta-1 isoform 3

    See identical proteins and their annotated locations for NP_001248755.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes the longer isoform (3).
    Source sequence(s)
    AB208804, AC005545, BM982261, HY040370
    Consensus CDS
    CCDS58638.1
    UniProtKB/Swiss-Prot
    O14617
    Related
    ENSP00000495274.1, ENST00000643116.2
    Conserved Domains (4) summary
    pfam01602
    Location:32581
    Adaptin_N; Adaptin N terminal region
    pfam06375
    Location:661807
    BLVR; Bovine leukaemia virus receptor (BLVR)
    pfam12717
    Location:155265
    Cnd1; non-SMC mitotic condensation complex subunit 1
    sd00044
    Location:151172
    HEAT; HEAT repeat [structural motif]
  2. NM_003938.8NP_003929.4  AP-3 complex subunit delta-1 isoform 2

    See identical proteins and their annotated locations for NP_003929.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 3' coding region compared to variant 3. The encoded isoform (2) is shorter than isoform 3.
    Source sequence(s)
    AC005545, AF002163, BM982261, HY040370
    Consensus CDS
    CCDS42459.1
    UniProtKB/Swiss-Prot
    O14617
    Related
    ENSP00000344055.4, ENST00000345016.9
    Conserved Domains (4) summary
    pfam01602
    Location:32581
    Adaptin_N; Adaptin N terminal region
    pfam06375
    Location:661807
    BLVR; Bovine leukaemia virus receptor (BLVR)
    pfam12717
    Location:155265
    Cnd1; non-SMC mitotic condensation complex subunit 1
    sd00044
    Location:151172
    HEAT; HEAT repeat [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    2100988..2151620 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006722932.2XP_006722995.1  AP-3 complex subunit delta-1 isoform X1

    Conserved Domains (4) summary
    pfam01602
    Location:32581
    Adaptin_N; Adaptin N terminal region
    pfam06375
    Location:661807
    BLVR; Bovine leukaemia virus receptor (BLVR)
    pfam12717
    Location:155265
    Cnd1; non-SMC mitotic condensation complex subunit 1
    sd00044
    Location:151172
    HEAT; HEAT repeat [structural motif]
  2. XM_017027422.1XP_016882911.1  AP-3 complex subunit delta-1 isoform X2

    Related
    ENSP00000494972.1, ENST00000644728.1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001077523.1: Suppressed sequence

    Description
    NM_001077523.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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