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Protein

AP-3 complex subunit delta-1

Gene

AP3D1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals.

GO - Molecular functioni

  • transporter activity Source: ProtInc

GO - Biological processi

  • anterograde axonal transport Source: UniProtKB
  • anterograde synaptic vesicle transport Source: UniProtKB
  • antigen processing and presentation, exogenous lipid antigen via MHC class Ib Source: Ensembl
  • endosome to melanosome transport Source: ParkinsonsUK-UCL
  • eye pigment biosynthetic process Source: ProtInc
  • intracellular protein transport Source: ProtInc
  • melanosome organization Source: ParkinsonsUK-UCL
  • positive regulation of NK T cell differentiation Source: Ensembl
  • protein localization to membrane Source: ParkinsonsUK-UCL
  • protein localization to organelle Source: Ensembl
  • regulation of sequestering of zinc ion Source: BHF-UCL
  • synaptic vesicle membrane organization Source: Ensembl
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Enzyme and pathway databases

BioCyciZFISH:ENSG00000065000-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
AP-3 complex subunit delta-1
Alternative name(s):
AP-3 complex subunit delta
Adaptor-related protein complex 3 subunit delta-1
Delta-adaptin
Gene namesi
Name:AP3D1
ORF Names:PRO0039
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:568. AP3D1.

Subcellular locationi

GO - Cellular componenti

  • AP-3 adaptor complex Source: InterPro
  • axon cytoplasm Source: GOC
  • endosome membrane Source: UniProtKB
  • Golgi apparatus Source: ProtInc
  • Golgi membrane Source: UniProtKB-SubCell
  • lysosomal membrane Source: UniProtKB
  • membrane Source: UniProtKB
  • nucleoplasm Source: HPA
  • terminal bouton Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Golgi apparatus, Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi8943.
OpenTargetsiENSG00000065000.
PharmGKBiPA24859.

Polymorphism and mutation databases

BioMutaiAP3D1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001937662 – 1153AP-3 complex subunit delta-1Add BLAST1152

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei632PhosphoserineCombined sources1
Modified residuei634PhosphoserineCombined sources1
Modified residuei636PhosphoserineCombined sources1
Modified residuei658PhosphoserineCombined sources1
Modified residuei688PhosphoserineCombined sources1
Modified residuei758PhosphoserineCombined sources1
Modified residuei759PhosphoserineCombined sources1
Modified residuei762PhosphothreonineCombined sources1
Modified residuei764PhosphoserineCombined sources1
Modified residuei788PhosphoserineCombined sources1
Modified residuei829PhosphoserineCombined sources1
Isoform 2 (identifier: O14617-2)
Modified residuei785PhosphoserineCombined sources1
Modified residuei828PhosphoserineCombined sources1
Isoform 5 (identifier: O14617-5)
Modified residuei931PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiO14617.
MaxQBiO14617.
PaxDbiO14617.
PeptideAtlasiO14617.
PRIDEiO14617.

PTM databases

iPTMnetiO14617.
PhosphoSitePlusiO14617.
SwissPalmiO14617.

Expressioni

Tissue specificityi

Present in all adult tissues examined with the highest levels in skeletal muscle, heart, pancreas and testis.1 Publication

Gene expression databases

BgeeiENSG00000065000.
CleanExiHS_AP3D1.
ExpressionAtlasiO14617. baseline and differential.
GenevisibleiO14617. HS.

Organism-specific databases

HPAiHPA047554.
HPA052776.

Interactioni

Subunit structurei

AP-3 associates with the BLOC-1 complex (By similarity). Adaptor protein complex 3 (AP-3) is a heterotetramer composed of two large adaptins (delta-type subunit AP3D1 and beta-type subunit AP3B1 or AP3B2), a medium adaptin (mu-type subunit AP3M1 or AP3M2) and a small adaptin (sigma-type subunit APS1 or AP3S2) (By similarity). Interacts with SLC30A2 (PubMed:25808614).By similarity1 Publication

Protein-protein interaction databases

BioGridi114455. 44 interactors.
DIPiDIP-46793N.
IntActiO14617. 19 interactors.
MINTiMINT-5003757.
STRINGi9606.ENSP00000344055.

Structurei

Secondary structure

11153
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi704 – 706Combined sources3
Beta strandi722 – 728Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4AFIX-ray2.80A/B680-729[»]
ProteinModelPortaliO14617.
SMRiO14617.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati34 – 71HEAT 1Add BLAST38
Repeati77 – 114HEAT 2Add BLAST38
Repeati142 – 179HEAT 3Add BLAST38
Repeati180 – 216HEAT 4Add BLAST37
Repeati254 – 292HEAT 5Add BLAST39
Repeati299 – 336HEAT 6Add BLAST38
Repeati338 – 373HEAT 7Add BLAST36
Repeati375 – 409HEAT 8Add BLAST35
Repeati431 – 468HEAT 9Add BLAST38
Repeati497 – 535HEAT 10Add BLAST39
Repeati548 – 585HEAT 11Add BLAST38

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili659 – 679Sequence analysisAdd BLAST21
Coiled coili725 – 756Sequence analysisAdd BLAST32
Coiled coili845 – 869Sequence analysisAdd BLAST25

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi828 – 893Lys-richAdd BLAST66

Sequence similaritiesi

Contains 11 HEAT repeats.Curated

Keywords - Domaini

Coiled coil, Repeat

Phylogenomic databases

eggNOGiKOG1059. Eukaryota.
ENOG410XQFB. LUCA.
GeneTreeiENSGT00550000075067.
HOGENOMiHOG000000981.
HOVERGENiHBG050520.
InParanoidiO14617.
KOiK12396.
OMAiKMTYDIQ.
OrthoDBiEOG091G04IL.
PhylomeDBiO14617.
TreeFamiTF105666.

Family and domain databases

Gene3Di1.25.10.10. 1 hit.
InterProiIPR010474. AP3D1.
IPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR002553. Clathrin/coatomer_adapt-like_N.
[Graphical view]
PfamiPF01602. Adaptin_N. 1 hit.
PF06375. AP3D1. 1 hit.
[Graphical view]
SMARTiSM01354. BLVR. 1 hit.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 1 hit.

Sequences (5)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O14617-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MALKMVKGSI DRMFDKNLQD LVRGIRNHKE DEAKYISQCI DEIKQELKQD
60 70 80 90 100
NIAVKANAVC KLTYLQMLGY DISWAAFNII EVMSASKFTF KRIGYLAASQ
110 120 130 140 150
SFHEGTDVIM LTTNQIRKDL SSPSQYDTGV ALTGLSCFVT PDLARDLAND
160 170 180 190 200
IMTLMSHTKP YIRKKAVLIM YKVFLKYPES LRPAFPRLKE KLEDPDPGVQ
210 220 230 240 250
SAAVNVICEL ARRNPKNYLS LAPLFFKLMT SSTNNWVLIK IIKLFGALTP
260 270 280 290 300
LEPRLGKKLI EPLTNLIHST SAMSLLYECV NTVIAVLISL SSGMPNHSAS
310 320 330 340 350
IQLCVQKLRI LIEDSDQNLK YLGLLAMSKI LKTHPKSVQS HKDLILQCLD
360 370 380 390 400
DKDESIRLRA LDLLYGMVSK KNLMEIVKKL MTHVDKAEGT TYRDELLTKI
410 420 430 440 450
IDICSQSNYQ YITNFEWYIS ILVELTRLEG TRHGHLIAAQ MLDVAIRVKA
460 470 480 490 500
IRKFAVSQMS ALLDSAHLLA SSTQRNGICE VLYAAAWICG EFSEHLQEPH
510 520 530 540 550
HTLEAMLRPR VTTLPGHIQA VYVQNVVKLY ASILQQKEQA GEAEGAQAVT
560 570 580 590 600
QLMVDRLPQF VQSADLEVQE RASCILQLVK HIQKLQAKDV PVAEEVSALF
610 620 630 640 650
AGELNPVAPK AQKKVPVPEG LDLDAWINEP LSDSESEDER PRAVFHEEEQ
660 670 680 690 700
RRPKHRPSEA DEEELARRRE ARKQEQANNP FYIKSSPSPQ KRYQDTPGVE
710 720 730 740 750
HIPVVQIDLS VPLKVPGLPM SDQYVKLEEE RRHRQKLEKD KRRKKRKEKE
760 770 780 790 800
KKGKRRHSSL PTESDEDIAP AQQVDIVTEE MPENALPSDE DDKDPNDPYR
810 820 830 840 850
ALDIDLDKPL ADSEKLPIQK HRNTETSKSP EKDVPMVEKK SKKPKKKEKK
860 870 880 890 900
HKEKERDKEK KKEKEKKKSP KPKKKKHRKE KEERTKGKKK SKKQPPGSEE
910 920 930 940 950
AAGEPVQNGA PEEEQLPPES SYSLLAENSY VKMTCDIRGS LQEDSQVTVA
960 970 980 990 1000
IVLENRSSSI LKGMELSVLD SLNARMARPQ GSSVHDGVPV PFQLPPGVSN
1010 1020 1030 1040 1050
EAQYVFTIQS IVMAQKLKGT LSFIAKNDEG ATHEKLDFRL HFSCSSYLIT
1060 1070 1080 1090 1100
TPCYSDAFAK LLESGDLSMS SIKVDGIRMS FQNLLAKICF HHHFSVVERV
1110 1120 1130 1140 1150
DSCASMYSRS IQGHHVCLLV KKGENSVSVD GKCSDSTLLS NLLEEMKATL

AKC
Length:1,153
Mass (Da):130,158
Last modified:January 1, 1998 - v1
Checksum:i1B491DD64EAD5096
GO
Isoform 2 (identifier: O14617-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     168-258: Missing.
     866-866: K → KKAEDLDFWLSTTPPPAPAPAPAPVPSTDECEDAKTEAQGEEDDAEGQDQD

Show »
Length:1,112
Mass (Da):125,040
Checksum:i33380E690D5AC35F
GO
Isoform 3 (identifier: O14617-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     117-285: Missing.

Show »
Length:984
Mass (Da):111,238
Checksum:i8FA5C9ED9EF57A83
GO
Isoform 4 (identifier: O14617-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     746-877: Missing.

Show »
Length:1,021
Mass (Da):114,707
Checksum:i730F9AD61CEF63DD
GO
Isoform 5 (identifier: O14617-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     866-866: K → KKAEDLDFWLSTTPPPAPAPAPAPVPSTGELSVNTVTTPKDECEDAKTEAQGEEDDAEGQDQD

Show »
Length:1,215
Mass (Da):136,651
Checksum:iE77257F13AD4A67F
GO

Sequence cautioni

The sequence AAG35473 differs from that shown. Contaminating sequence. Presence of an unrelated sequence found on chromosome 7.Curated
The sequence AAH10065 differs from that shown. Lack of 8 exons and truncation of 2 other exons in the C- terminus. Alternative splicing seems doubtful, since exon-intron junctions are not the consensus ones.Curated
The sequence BAD92041 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti3L → F in AAD03777 (PubMed:9151686).Curated1
Sequence conflicti167Missing in AAC34214 (PubMed:15057824).Curated1
Sequence conflicti252E → G in AAH10065 (PubMed:15489334).Curated1
Sequence conflicti595 – 603EVSALFAGE → DFVHCCYEL in AAG35473 (Ref. 6) Curated9

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_033517541G → R.Corresponds to variant rs34569645dbSNPEnsembl.1
Natural variantiVAR_0335181072I → V.Corresponds to variant rs25673dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_000167117 – 285Missing in isoform 3. 1 PublicationAdd BLAST169
Alternative sequenceiVSP_000165168 – 258Missing in isoform 2. 2 PublicationsAdd BLAST91
Alternative sequenceiVSP_000168746 – 877Missing in isoform 4. 1 PublicationAdd BLAST132
Alternative sequenceiVSP_000166866K → KKAEDLDFWLSTTPPPAPAP APAPVPSTDECEDAKTEAQG EEDDAEGQDQD in isoform 2. 2 Publications1
Alternative sequenceiVSP_017106866K → KKAEDLDFWLSTTPPPAPAP APAPVPSTGELSVNTVTTPK DECEDAKTEAQGEEDDAEGQ DQD in isoform 5. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF002163 mRNA. Translation: AAC51761.1.
U91930 mRNA. Translation: AAD03777.1.
AB208804 mRNA. Translation: BAD92041.1. Different initiation.
AC005545 Genomic DNA. Translation: AAC34212.1.
AC005545 Genomic DNA. Translation: AAC34214.1.
BC010065 mRNA. Translation: AAH10065.1. Sequence problems.
AF130042 mRNA. Translation: AAG35473.1. Sequence problems.
CCDSiCCDS42459.1. [O14617-1]
CCDS58638.1. [O14617-5]
RefSeqiNP_001248755.1. NM_001261826.1. [O14617-5]
NP_003929.4. NM_003938.6. [O14617-1]
UniGeneiHs.512815.

Genome annotation databases

EnsembliENST00000345016; ENSP00000344055; ENSG00000065000. [O14617-1]
ENST00000355272; ENSP00000347416; ENSG00000065000. [O14617-5]
GeneIDi8943.
KEGGihsa:8943.
UCSCiuc002luz.4. human. [O14617-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF002163 mRNA. Translation: AAC51761.1.
U91930 mRNA. Translation: AAD03777.1.
AB208804 mRNA. Translation: BAD92041.1. Different initiation.
AC005545 Genomic DNA. Translation: AAC34212.1.
AC005545 Genomic DNA. Translation: AAC34214.1.
BC010065 mRNA. Translation: AAH10065.1. Sequence problems.
AF130042 mRNA. Translation: AAG35473.1. Sequence problems.
CCDSiCCDS42459.1. [O14617-1]
CCDS58638.1. [O14617-5]
RefSeqiNP_001248755.1. NM_001261826.1. [O14617-5]
NP_003929.4. NM_003938.6. [O14617-1]
UniGeneiHs.512815.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4AFIX-ray2.80A/B680-729[»]
ProteinModelPortaliO14617.
SMRiO14617.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114455. 44 interactors.
DIPiDIP-46793N.
IntActiO14617. 19 interactors.
MINTiMINT-5003757.
STRINGi9606.ENSP00000344055.

PTM databases

iPTMnetiO14617.
PhosphoSitePlusiO14617.
SwissPalmiO14617.

Polymorphism and mutation databases

BioMutaiAP3D1.

Proteomic databases

EPDiO14617.
MaxQBiO14617.
PaxDbiO14617.
PeptideAtlasiO14617.
PRIDEiO14617.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000345016; ENSP00000344055; ENSG00000065000. [O14617-1]
ENST00000355272; ENSP00000347416; ENSG00000065000. [O14617-5]
GeneIDi8943.
KEGGihsa:8943.
UCSCiuc002luz.4. human. [O14617-1]

Organism-specific databases

CTDi8943.
DisGeNETi8943.
GeneCardsiAP3D1.
H-InvDBHIX0014607.
HGNCiHGNC:568. AP3D1.
HPAiHPA047554.
HPA052776.
MIMi607246. gene.
neXtProtiNX_O14617.
OpenTargetsiENSG00000065000.
PharmGKBiPA24859.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1059. Eukaryota.
ENOG410XQFB. LUCA.
GeneTreeiENSGT00550000075067.
HOGENOMiHOG000000981.
HOVERGENiHBG050520.
InParanoidiO14617.
KOiK12396.
OMAiKMTYDIQ.
OrthoDBiEOG091G04IL.
PhylomeDBiO14617.
TreeFamiTF105666.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000065000-MONOMER.

Miscellaneous databases

ChiTaRSiAP3D1. human.
GeneWikiiAP3D1.
GenomeRNAii8943.
PROiO14617.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000065000.
CleanExiHS_AP3D1.
ExpressionAtlasiO14617. baseline and differential.
GenevisibleiO14617. HS.

Family and domain databases

Gene3Di1.25.10.10. 1 hit.
InterProiIPR010474. AP3D1.
IPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR002553. Clathrin/coatomer_adapt-like_N.
[Graphical view]
PfamiPF01602. Adaptin_N. 1 hit.
PF06375. AP3D1. 1 hit.
[Graphical view]
SMARTiSM01354. BLVR. 1 hit.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiAP3D1_HUMAN
AccessioniPrimary (citable) accession number: O14617
Secondary accession number(s): O00202
, O75262, Q59HF5, Q96G11, Q9H3C6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 11, 2002
Last sequence update: January 1, 1998
Last modified: November 30, 2016
This is version 163 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.