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Q5T1V6

- DDX59_HUMAN

UniProt

Q5T1V6 - DDX59_HUMAN

Protein

Probable ATP-dependent RNA helicase DDX59

Gene

DDX59

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 101 (01 Oct 2014)
      Sequence version 1 (21 Dec 2004)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    ATP + H2O = ADP + phosphate.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri104 – 13330HIT-typeAdd
    BLAST
    Nucleotide bindingi247 – 2548ATPPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. helicase activity Source: UniProtKB-KW
    3. metal ion binding Source: UniProtKB-KW
    4. RNA binding Source: UniProtKB-KW

    Keywords - Molecular functioni

    Helicase, Hydrolase

    Keywords - Ligandi

    ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Probable ATP-dependent RNA helicase DDX59 (EC:3.6.4.13)
    Alternative name(s):
    DEAD box protein 59
    Zinc finger HIT domain-containing protein 5
    Gene namesi
    Name:DDX59
    Synonyms:ZNHIT5
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 1

    Organism-specific databases

    HGNCiHGNC:25360. DDX59.

    Subcellular locationi

    Cytoplasm 1 Publication. Nucleus 1 Publication
    Note: Exhibits granular localization in the nucleus, as well as in the cytoplasm.

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. intracellular Source: LIFEdb
    3. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Involvement in diseasei

    Orofaciodigital syndrome 5 (OFD5) [MIM:174300]: A form of orofaciodigital syndrome, a group of heterogeneous disorders characterized by malformations of the oral cavity, face and digits, and associated phenotypic abnormalities that lead to the delineation of various subtypes. OFD5 patients show the core features of cleft palate, lobulated tongue, and polydactyly. Additional features include frontal bossing and intellectual disability.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti367 – 3671V → G in OFD5; markedly reduced expression in fibroblasts compared to wild-type protein; impaired SHH signaling in SAG-treated fibroblasts. 1 Publication
    VAR_070198
    Natural varianti534 – 5341G → R in OFD5. 1 Publication
    VAR_070199

    Keywords - Diseasei

    Ciliopathy, Disease mutation

    Organism-specific databases

    MIMi174300. phenotype.
    Orphaneti369902. Orofaciodigital syndrome type 14.
    PharmGKBiPA142672000.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 619619Probable ATP-dependent RNA helicase DDX59PRO_0000282713Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei64 – 641Phosphoserine1 Publication
    Modified residuei160 – 1601Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ5T1V6.
    PaxDbiQ5T1V6.
    PRIDEiQ5T1V6.

    PTM databases

    PhosphoSiteiQ5T1V6.

    Expressioni

    Tissue specificityi

    Expressed in fibroblasts (at protein level).1 Publication

    Gene expression databases

    ArrayExpressiQ5T1V6.
    BgeeiQ5T1V6.
    CleanExiHS_DDX59.
    GenevestigatoriQ5T1V6.

    Organism-specific databases

    HPAiHPA047166.

    Interactioni

    Protein-protein interaction databases

    MINTiMINT-4714465.
    STRINGi9606.ENSP00000330460.

    Structurei

    Secondary structure

    1
    619
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi109 – 1135
    Beta strandi116 – 1183
    Beta strandi120 – 1223
    Beta strandi125 – 1284
    Helixi129 – 14315

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2YQPNMR-A94-146[»]
    ProteinModelPortaliQ5T1V6.
    SMRiQ5T1V6. Positions 96-146, 168-581.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5T1V6.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini234 – 405172Helicase ATP-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini416 – 579164Helicase C-terminalPROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi203 – 23129Q motifAdd
    BLAST
    Motifi353 – 3564DEAD box

    Domaini

    The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.

    Sequence similaritiesi

    Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
    Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation
    Contains 1 HIT-type zinc finger.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri104 – 13330HIT-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG0513.
    HOGENOMiHOG000006599.
    HOVERGENiHBG106120.
    InParanoidiQ5T1V6.
    OMAiEHPFILN.
    OrthoDBiEOG7B8S3D.
    PhylomeDBiQ5T1V6.
    TreeFamiTF330866.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
    IPR014001. Helicase_ATP-bd.
    IPR001650. Helicase_C.
    IPR027417. P-loop_NTPase.
    IPR014014. RNA_helicase_DEAD_Q_motif.
    IPR007529. Znf_HIT.
    [Graphical view]
    PfamiPF00270. DEAD. 1 hit.
    PF00271. Helicase_C. 1 hit.
    PF04438. zf-HIT. 1 hit.
    [Graphical view]
    SMARTiSM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 2 hits.
    PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS51194. HELICASE_CTER. 1 hit.
    PS51195. Q_MOTIF. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q5T1V6-1) [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

    MFVPRSLKIK RNANDDGKSC VAKIIKPDPE DLQLDKSRDV PVDAVATEAA    50
    TIDRHISESC PFPSPGGQLA EVHSVSPEQG AKDSHPSEEP VKSFSKTQRW 100
    AEPGEPICVV CGRYGEYICD KTDEDVCSLE CKAKHLLQVK EKEEKSKLSN 150
    PQKADSEPES PLNASYVYKE HPFILNLQED QIENLKQQLG ILVQGQEVTR 200
    PIIDFEHCSL PEVLNHNLKK SGYEVPTPIQ MQMIPVGLLG RDILASADTG 250
    SGKTAAFLLP VIMRALFESK TPSALILTPT RELAIQIERQ AKELMSGLPR 300
    MKTVLLVGGL PLPPQLYRLQ QHVKVIIATP GRLLDIIKQS SVELCGVKIV 350
    VVDEADTMLK MGFQQQVLDI LENIPNDCQT ILVSATIPTS IEQLASQLLH 400
    NPVRIITGEK NLPCANVRQI ILWVEDPAKK KKLFEILNDK KLFKPPVLVF 450
    VDCKLGADLL SEAVQKITGL KSISIHSEKS QIERKNILKG LLEGDYEVVV 500
    STGVLGRGLD LISVRLVVNF DMPSSMDEYV HQIGRVGRLG QNGTAITFIN 550
    NNSKRLFWDI AKRVKPTGSI LPPQLLNSPY LHDQKRKEQQ KDKQTQNDLV 600
    TGANLMDIIR KHDKSNSQK 619
    Length:619
    Mass (Da):68,810
    Last modified:December 21, 2004 - v1
    Checksum:i2B4EE96C11CB48ED
    GO
    Isoform 2 (identifier: Q5T1V6-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         533-619: IGRVGRLGQN...RKHDKSNSQK → ENTYKSTWRN...KLGLKKNCSS

    Note: No experimental confirmation available.

    Show »
    Length:580
    Mass (Da):64,572
    Checksum:i11BD25D69906898E
    GO

    Sequence cautioni

    The sequence AAH14183.1 differs from that shown. Reason: Contaminating sequence. Potential poly-A sequence starting in position 433.

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti77 – 771P → T in a breast cancer sample; somatic mutation. 1 Publication
    VAR_035842
    Natural varianti107 – 1071I → V.
    Corresponds to variant rs3795634 [ dbSNP | Ensembl ].
    VAR_031424
    Natural varianti367 – 3671V → G in OFD5; markedly reduced expression in fibroblasts compared to wild-type protein; impaired SHH signaling in SAG-treated fibroblasts. 1 Publication
    VAR_070198
    Natural varianti472 – 4721S → R.1 Publication
    Corresponds to variant rs17854157 [ dbSNP | Ensembl ].
    VAR_033001
    Natural varianti534 – 5341G → R in OFD5. 1 Publication
    VAR_070199

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei533 – 61987IGRVG…SNSQK → ENTYKSTWRNPQHFQQDVRM TLGYVGKAQWEEDNQLKVKL GLKKNCSS in isoform 2. 1 PublicationVSP_024227Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL136611 mRNA. Translation: CAB66546.1.
    AL445483 Genomic DNA. Translation: CAI17055.1.
    AL445483 Genomic DNA. Translation: CAI17056.1.
    BC014183 mRNA. Translation: AAH14183.1. Sequence problems.
    BC041801 mRNA. Translation: AAH41801.1.
    CCDSiCCDS30964.1. [Q5T1V6-1]
    RefSeqiNP_001026895.2. NM_001031725.4. [Q5T1V6-1]
    UniGeneiHs.497332.

    Genome annotation databases

    EnsembliENST00000331314; ENSP00000330460; ENSG00000118197. [Q5T1V6-1]
    ENST00000447706; ENSP00000394367; ENSG00000118197. [Q5T1V6-2]
    GeneIDi83479.
    KEGGihsa:83479.
    UCSCiuc009wzk.3. human. [Q5T1V6-1]

    Polymorphism databases

    DMDMi74762230.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL136611 mRNA. Translation: CAB66546.1 .
    AL445483 Genomic DNA. Translation: CAI17055.1 .
    AL445483 Genomic DNA. Translation: CAI17056.1 .
    BC014183 mRNA. Translation: AAH14183.1 . Sequence problems.
    BC041801 mRNA. Translation: AAH41801.1 .
    CCDSi CCDS30964.1. [Q5T1V6-1 ]
    RefSeqi NP_001026895.2. NM_001031725.4. [Q5T1V6-1 ]
    UniGenei Hs.497332.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2YQP NMR - A 94-146 [» ]
    ProteinModelPortali Q5T1V6.
    SMRi Q5T1V6. Positions 96-146, 168-581.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    MINTi MINT-4714465.
    STRINGi 9606.ENSP00000330460.

    PTM databases

    PhosphoSitei Q5T1V6.

    Polymorphism databases

    DMDMi 74762230.

    Proteomic databases

    MaxQBi Q5T1V6.
    PaxDbi Q5T1V6.
    PRIDEi Q5T1V6.

    Protocols and materials databases

    DNASUi 83479.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000331314 ; ENSP00000330460 ; ENSG00000118197 . [Q5T1V6-1 ]
    ENST00000447706 ; ENSP00000394367 ; ENSG00000118197 . [Q5T1V6-2 ]
    GeneIDi 83479.
    KEGGi hsa:83479.
    UCSCi uc009wzk.3. human. [Q5T1V6-1 ]

    Organism-specific databases

    CTDi 83479.
    GeneCardsi GC01M200594.
    HGNCi HGNC:25360. DDX59.
    HPAi HPA047166.
    MIMi 174300. phenotype.
    615464. gene.
    neXtProti NX_Q5T1V6.
    Orphaneti 369902. Orofaciodigital syndrome type 14.
    PharmGKBi PA142672000.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG0513.
    HOGENOMi HOG000006599.
    HOVERGENi HBG106120.
    InParanoidi Q5T1V6.
    OMAi EHPFILN.
    OrthoDBi EOG7B8S3D.
    PhylomeDBi Q5T1V6.
    TreeFami TF330866.

    Miscellaneous databases

    EvolutionaryTracei Q5T1V6.
    GeneWikii DDX59.
    GenomeRNAii 83479.
    NextBioi 72419.
    PROi Q5T1V6.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q5T1V6.
    Bgeei Q5T1V6.
    CleanExi HS_DDX59.
    Genevestigatori Q5T1V6.

    Family and domain databases

    Gene3Di 3.40.50.300. 2 hits.
    InterProi IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
    IPR014001. Helicase_ATP-bd.
    IPR001650. Helicase_C.
    IPR027417. P-loop_NTPase.
    IPR014014. RNA_helicase_DEAD_Q_motif.
    IPR007529. Znf_HIT.
    [Graphical view ]
    Pfami PF00270. DEAD. 1 hit.
    PF00271. Helicase_C. 1 hit.
    PF04438. zf-HIT. 1 hit.
    [Graphical view ]
    SMARTi SM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 2 hits.
    PROSITEi PS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS51194. HELICASE_CTER. 1 hit.
    PS51195. Q_MOTIF. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Fetal brain.
    2. "The DNA sequence and biological annotation of human chromosome 1."
      Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
      , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
      Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    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] (ISOFORM 1), VARIANT ARG-472.
      Tissue: Brain and Lung.
    4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-64, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    5. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
      Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
      Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-160, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Leukemic T-cell.
    6. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
      Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
      Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Solution structure of the ZF-hit domain in DEAD (Asp-Glu-Ala-Asp) box polypeptide 59."
      RIKEN structural genomics initiative (RSGI)
      Submitted (FEB-2009) to the PDB data bank
      Cited for: STRUCTURE BY NMR OF 94-146.
    9. Cited for: VARIANT [LARGE SCALE ANALYSIS] THR-77.
    10. "Mutations in DDX59 implicate RNA helicase in the pathogenesis of orofaciodigital syndrome."
      Shamseldin H.E., Rajab A., Alhashem A., Shaheen R., Al-Shidi T., Alamro R., Al Harassi S., Alkuraya F.S.
      Am. J. Hum. Genet. 93:555-560(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANTS OFD5 GLY-367 AND ARG-534, CHARACTERIZATION OF VARIANT OFD5 GLY-367, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.

    Entry informationi

    Entry nameiDDX59_HUMAN
    AccessioniPrimary (citable) accession number: Q5T1V6
    Secondary accession number(s): Q6PJL2, Q8IVW3, Q9H0W3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 3, 2007
    Last sequence update: December 21, 2004
    Last modified: October 1, 2014
    This is version 101 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 1
      Human chromosome 1: 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