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O95716

- RAB3D_HUMAN

UniProt

O95716 - RAB3D_HUMAN

Protein

Ras-related protein Rab-3D

Gene

RAB3D

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 137 (01 Oct 2014)
      Sequence version 1 (01 May 1999)
      Previous versions | rss
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    Functioni

    Protein transport. Probably involved in regulated exocytosis By similarity.By similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi29 – 379GTP
    Nucleotide bindingi77 – 815GTPBy similarity
    Nucleotide bindingi135 – 1384GTP
    Nucleotide bindingi165 – 1673GTP

    GO - Molecular functioni

    1. GTPase activity Source: ProtInc
    2. GTP binding Source: UniProtKB-KW

    GO - Biological processi

    1. exocytosis Source: UniProtKB-KW
    2. GTP catabolic process Source: GOC
    3. peptidyl-cysteine methylation Source: Ensembl
    4. protein transport Source: UniProtKB-KW
    5. regulation of exocytosis Source: Ensembl
    6. small GTPase mediated signal transduction Source: InterPro

    Keywords - Biological processi

    Exocytosis, Protein transport, Transport

    Keywords - Ligandi

    GTP-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ras-related protein Rab-3D
    Gene namesi
    Name:RAB3D
    Synonyms:GOV, RAB16
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 19

    Organism-specific databases

    HGNCiHGNC:9779. RAB3D.

    Subcellular locationi

    Cell membrane Curated; Lipid-anchor Curated; Cytoplasmic side Curated

    GO - Cellular componenti

    1. extracellular vesicular exosome Source: UniProt
    2. mitochondrion Source: Ensembl
    3. plasma membrane Source: UniProtKB-SubCell
    4. transport vesicle Source: Ensembl
    5. zymogen granule Source: Ensembl

    Keywords - Cellular componenti

    Cell membrane, Membrane

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA34134.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 219218Ras-related protein Rab-3DPRO_0000121088Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanine1 Publication
    Lipidationi217 – 2171S-geranylgeranyl cysteineBy similarity
    Modified residuei219 – 2191Cysteine methyl esterBy similarity
    Lipidationi219 – 2191S-geranylgeranyl cysteineBy similarity

    Keywords - PTMi

    Acetylation, Lipoprotein, Methylation, Prenylation

    Proteomic databases

    MaxQBiO95716.
    PaxDbiO95716.
    PRIDEiO95716.

    PTM databases

    PhosphoSiteiO95716.

    Expressioni

    Tissue specificityi

    Highly expressed in granulocytes of peripheral blood. Constitutively expressed at low levels in all hematopoietic cell lines investigated.

    Inductioni

    Activated in myeloid differentiation.

    Gene expression databases

    BgeeiO95716.
    CleanExiHS_RAB3D.
    GenevestigatoriO95716.

    Organism-specific databases

    HPAiCAB018067.
    HPA051912.

    Interactioni

    Subunit structurei

    Interacts with RIMS1, RIMS2, RPH3A, RPH3AL and RAB3IP.By similarity

    Protein-protein interaction databases

    BioGridi114919. 12 interactions.
    IntActiO95716. 3 interactions.
    STRINGi9606.ENSP00000222120.

    Structurei

    Secondary structure

    1
    219
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi20 – 289
    Helixi35 – 4410
    Beta strandi58 – 669
    Beta strandi69 – 779
    Helixi88 – 925
    Beta strandi96 – 1038
    Helixi107 – 1115
    Helixi113 – 12311
    Beta strandi129 – 1357
    Helixi140 – 1423
    Helixi147 – 15711
    Beta strandi160 – 1634
    Turni166 – 1694
    Helixi172 – 18716

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GF9X-ray1.53A20-189[»]
    ProteinModelPortaliO95716.
    SMRiO95716. Positions 20-189.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO95716.

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi51 – 599Effector regionBy similarity

    Sequence similaritiesi

    Belongs to the small GTPase superfamily. Rab family.Curated

    Phylogenomic databases

    eggNOGiCOG1100.
    HOGENOMiHOG000233968.
    HOVERGENiHBG009351.
    InParanoidiO95716.
    KOiK07884.
    OMAiEPSSCSC.
    OrthoDBiEOG7JQBPC.
    PhylomeDBiO95716.
    TreeFamiTF313199.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR027417. P-loop_NTPase.
    IPR005225. Small_GTP-bd_dom.
    IPR001806. Small_GTPase.
    IPR003579. Small_GTPase_Rab_type.
    [Graphical view]
    PfamiPF00071. Ras. 1 hit.
    [Graphical view]
    PRINTSiPR00449. RASTRNSFRMNG.
    SMARTiSM00175. RAB. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00231. small_GTP. 1 hit.
    PROSITEiPS51419. RAB. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    O95716-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASAGDTQAG PRDAADQNFD YMFKLLLIGN SSVGKTSFLF RYADDSFTPA    50
    FVSTVGIDFK VKTVYRHDKR IKLQIWDTAG QERYRTITTA YYRGAMGFLL 100
    MYDIANQESF AAVQDWATQI KTYSWDNAQV ILVGNKCDLE DERVVPAEDG 150
    RRLADDLGFE FFEASAKENI NVKQVFERLV DVICEKMNES LEPSSSSGSN 200
    GKGPAVGDAP APQPSSCSC 219
    Length:219
    Mass (Da):24,267
    Last modified:May 1, 1999 - v1
    Checksum:i714754826C405EA7
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti64 – 641V → I.
    Corresponds to variant rs3969860 [ dbSNP | Ensembl ].
    VAR_051710

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF081353 mRNA. Translation: AAC72918.1.
    AF498933 mRNA. Translation: AAM21081.1.
    BC016471 mRNA. Translation: AAH16471.1.
    CCDSiCCDS12257.1.
    RefSeqiNP_004274.1. NM_004283.3.
    UniGeneiHs.744916.

    Genome annotation databases

    EnsembliENST00000222120; ENSP00000222120; ENSG00000105514.
    ENST00000589655; ENSP00000466000; ENSG00000105514.
    GeneIDi9545.
    KEGGihsa:9545.
    UCSCiuc002mqx.3. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF081353 mRNA. Translation: AAC72918.1 .
    AF498933 mRNA. Translation: AAM21081.1 .
    BC016471 mRNA. Translation: AAH16471.1 .
    CCDSi CCDS12257.1.
    RefSeqi NP_004274.1. NM_004283.3.
    UniGenei Hs.744916.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2GF9 X-ray 1.53 A 20-189 [» ]
    ProteinModelPortali O95716.
    SMRi O95716. Positions 20-189.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 114919. 12 interactions.
    IntActi O95716. 3 interactions.
    STRINGi 9606.ENSP00000222120.

    PTM databases

    PhosphoSitei O95716.

    Proteomic databases

    MaxQBi O95716.
    PaxDbi O95716.
    PRIDEi O95716.

    Protocols and materials databases

    DNASUi 9545.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000222120 ; ENSP00000222120 ; ENSG00000105514 .
    ENST00000589655 ; ENSP00000466000 ; ENSG00000105514 .
    GeneIDi 9545.
    KEGGi hsa:9545.
    UCSCi uc002mqx.3. human.

    Organism-specific databases

    CTDi 9545.
    GeneCardsi GC19M011435.
    HGNCi HGNC:9779. RAB3D.
    HPAi CAB018067.
    HPA051912.
    MIMi 604350. gene.
    neXtProti NX_O95716.
    PharmGKBi PA34134.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG1100.
    HOGENOMi HOG000233968.
    HOVERGENi HBG009351.
    InParanoidi O95716.
    KOi K07884.
    OMAi EPSSCSC.
    OrthoDBi EOG7JQBPC.
    PhylomeDBi O95716.
    TreeFami TF313199.

    Miscellaneous databases

    EvolutionaryTracei O95716.
    GeneWikii RAB3D.
    GenomeRNAii 9545.
    NextBioi 35795.
    PROi O95716.
    SOURCEi Search...

    Gene expression databases

    Bgeei O95716.
    CleanExi HS_RAB3D.
    Genevestigatori O95716.

    Family and domain databases

    Gene3Di 3.40.50.300. 1 hit.
    InterProi IPR027417. P-loop_NTPase.
    IPR005225. Small_GTP-bd_dom.
    IPR001806. Small_GTPase.
    IPR003579. Small_GTPase_Rab_type.
    [Graphical view ]
    Pfami PF00071. Ras. 1 hit.
    [Graphical view ]
    PRINTSi PR00449. RASTRNSFRMNG.
    SMARTi SM00175. RAB. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 1 hit.
    TIGRFAMsi TIGR00231. small_GTP. 1 hit.
    PROSITEi PS51419. RAB. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Molecular cloning of cDNA encoding human Rab3D whose expression is upregulated with myeloid differentiation."
      Nishio H., Suda T., Sawada K., Miyamoto T., Koike T., Yamaguchi Y.
      Biochim. Biophys. Acta 1444:283-290(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Tissue: Hematopoietic.
    2. "cDNA clones of human proteins involved in signal transduction sequenced by the Guthrie cDNA resource center (www.cdna.org)."
      Puhl H.L. III, Ikeda S.R., Aronstam R.S.
      Submitted (APR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain.
    3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Ovary.
    4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    5. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
    6. "Crystal structure of human RAB3D in complex with GDP."
      Structural genomics consortium (SGC)
      Submitted (FEB-2009) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS) OF 20-189 IN COMPLEX WITH GDP.

    Entry informationi

    Entry nameiRAB3D_HUMAN
    AccessioniPrimary (citable) accession number: O95716
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1999
    Last sequence update: May 1, 1999
    Last modified: October 1, 2014
    This is version 137 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

    External Data

    Dasty 3