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Protein

Double-stranded RNA-binding protein 1

Gene

DRB1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Double-stranded RNA-binding protein involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the microRNAs (miRNAs) biogenesis by assisting DICER-LIKE 1 (DCL1) in the accurate processing from primary miRNAs (pri-miRNAs) to miRNAs in the nucleus. Forms a complex with SERRATE (SE) and DCL1 to promote accurate processing of pri-miRNAs by DCL1. Binds and assist DCL1 for accurate processing of precursor miRNAs (pre-miRNA). Indirectly involved in the production of trans-acting small interfering RNAs (ta-siRNAs) derived from the TAS1, TAS2 or TAS3 endogenous transcripts by participating in the production of their initiating miRNAs. Involved with argonaute 1 (AGO1) in the guide strand selection from miRNA duplexes, presumably by directional loading of the miRNA duplex (guide stand and passenger strand) onto the RNA-induced silencing complex (RISC) for passenger strand degradation. Does not participate in sense transgene-induced post-transcriptional gene silencing (S-PTGS). Involved in several plant development aspects and response to hormones through its role in miRNAs processing.12 Publications

GO - Molecular functioni

  • double-stranded RNA binding Source: TAIR
  • miRNA binding Source: TAIR
  • ribonuclease III activity Source: GO_Central

GO - Biological processi

  • leaf proximal/distal pattern formation Source: TAIR
  • leaf vascular tissue pattern formation Source: TAIR
  • mRNA cleavage involved in gene silencing by miRNA Source: TAIR
  • pre-miRNA processing Source: UniProtKB
  • primary miRNA processing Source: GO_Central
  • production of miRNAs involved in gene silencing by miRNA Source: TAIR
  • production of ta-siRNAs involved in RNA interference Source: TAIR
  • response to abscisic acid Source: TAIR
  • response to auxin Source: TAIR
  • response to cytokinin Source: TAIR
  • RNA phosphodiester bond hydrolysis, endonucleolytic Source: GO_Central
Complete GO annotation...

Keywords - Biological processi

RNA-mediated gene silencing

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Double-stranded RNA-binding protein 1
Alternative name(s):
Protein HYPONASTIC LEAVES 1
dsRNA-binding protein 1
Short name:
AtDRB1
Gene namesi
Name:DRB1
Synonyms:HYL1
Ordered Locus Names:At1g09700
ORF Names:F21M12.9
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G09700.

Subcellular locationi

GO - Cellular componenti

  • nuclear dicing body Source: TAIR
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Short plant, delayed flowering, leaf hyponasty, reduced fertility, decreased rate of root growth, altered root gravitropic response, decreased sensitivity to auxin and cytokinin and hypersensitivity to abscisic acid (ABA). Reduction of several miRNA accumulation.3 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 419419Double-stranded RNA-binding protein 1PRO_0000404652Add
BLAST

Proteomic databases

PaxDbiO04492.
PRIDEiO04492.

PTM databases

iPTMnetiO04492.

Expressioni

Tissue specificityi

Expressed in rosette and cauline leaves, stems, roots, flowers and siliques.2 Publications

Inductioni

By abscisic acid (ABA).1 Publication

Gene expression databases

GenevisibleiO04492. AT.

Interactioni

Subunit structurei

Homodimer. Heterodimer with DRB2, DRB4 or DRB5. Interacts with SE and DCL1.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
At3g03300Q3EBC82EBI-632620,EBI-2464030
DCL1Q9SP323EBI-632620,EBI-632627
DRB5Q8GY794EBI-632620,EBI-632672
SEQ9ZVD05EBI-632620,EBI-6553299

Protein-protein interaction databases

BioGridi22739. 19 interactions.
DIPiDIP-33453N.
IntActiO04492. 6 interactions.
STRINGi3702.AT1G09700.1.

Structurei

Secondary structure

1
419
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi16 – 2611Combined sources
Beta strandi33 – 419Combined sources
Beta strandi42 – 443Combined sources
Beta strandi46 – 538Combined sources
Beta strandi56 – 594Combined sources
Beta strandi64 – 663Combined sources
Helixi67 – 8216Combined sources
Helixi100 – 11112Combined sources
Turni112 – 1143Combined sources
Beta strandi119 – 1268Combined sources
Beta strandi128 – 1303Combined sources
Beta strandi132 – 1409Combined sources
Beta strandi143 – 1464Combined sources
Beta strandi150 – 1523Combined sources
Helixi153 – 16917Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2L2MNMR-A97-170[»]
2L2NNMR-A1-100[»]
3ADGX-ray1.70A15-84[»]
3ADIX-ray3.20A/B/C15-84[»]
3ADJX-ray3.00A100-172[»]
ProteinModelPortaliO04492.
SMRiO04492. Positions 16-86, 100-170.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO04492.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini15 – 8470DRBM 1PROSITE-ProRule annotationAdd
BLAST
Domaini101 – 17070DRBM 2PROSITE-ProRule annotationAdd
BLAST
Repeati247 – 274281Add
BLAST
Repeati275 – 302282Add
BLAST
Repeati303 – 330283Add
BLAST
Repeati331 – 358284Add
BLAST
Repeati359 – 386285Add
BLAST
Repeati387 – 414286Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni247 – 4141686 X 28 AA repeats of E-K-I-E-T-T-P-N-L-E-[PS]-[PS]-S-C-M-[NS]-G-L-K-E-A-A-F-G-S-V-E-TAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi207 – 22216Bipartite nuclear localizationAdd
BLAST

Domaini

The dsRNA binding domains (dsRBDs) 1 and 2 are sufficient for the function in miRNA precursors processing and mature miRNA generation.3 Publications

Sequence similaritiesi

Contains 2 DRBM (double-stranded RNA-binding) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410IWVA. Eukaryota.
ENOG4111ZFG. LUCA.
InParanoidiO04492.
OMAiCMNGLKE.

Family and domain databases

Gene3Di3.30.160.20. 2 hits.
InterProiIPR014720. dsRBD_dom.
[Graphical view]
PfamiPF00035. dsrm. 2 hits.
[Graphical view]
SMARTiSM00358. DSRM. 2 hits.
[Graphical view]
PROSITEiPS50137. DS_RBD. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O04492-1) [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
MTSTDVSSGV SNCYVFKSRL QEYAQKYKLP TPVYEIVKEG PSHKSLFQST
60 70 80 90 100
VILDGVRYNS LPGFFNRKAA EQSAAEVALR ELAKSSELSQ CVSQPVHETG
110 120 130 140 150
LCKNLLQEYA QKMNYAIPLY QCQKVETLGR VTQFTCTVEI GGIKYTGAAT
160 170 180 190 200
RTKKDAEISA GRTALLAIQS DTKNNLANYN TQLTVLPCEK KTIQAAIPLK
210 220 230 240 250
ETVKTLKARK AQFKKKAQKG KRTVAKNPED IIIPPQPTDH CQNDQSEKIE
260 270 280 290 300
TTPNLEPSSC MNGLKEAAFG SVETEKIETT PNLEPPSCMN GLKEAAFGSV
310 320 330 340 350
ETEKIETTPN LEPPSCMNGL KEAAFGSVET EKIETTPNLE PSSCMNGLKE
360 370 380 390 400
AAFGSVETEK IETTPNLEPP SCMNGLKEAA FGSVETEKIE TTPNLESSSC
410
MSGLKEAAFG SVETEASHA
Length:419
Mass (Da):45,547
Last modified:July 1, 1997 - v1
Checksum:iFDBE165679537DFB
GO
Isoform 2 (identifier: O04492-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     72-87: Missing.

Note: No experimental confirmation available.
Show »
Length:403
Mass (Da):43,876
Checksum:i5866B3A8C7582213
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei72 – 8716Missing in isoform 2. 1 PublicationVSP_040613Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF276440 mRNA. Translation: AAG49890.1.
AC000132 Genomic DNA. Translation: AAB60726.1.
CP002684 Genomic DNA. Translation: AEE28481.1.
AY054631 mRNA. Translation: AAK96822.1.
AY081525 mRNA. Translation: AAM10087.1.
AK319123 mRNA. Translation: BAH57238.1.
PIRiH86230.
RefSeqiNP_563850.1. NM_100842.3. [O04492-1]
UniGeneiAt.10223.

Genome annotation databases

EnsemblPlantsiAT1G09700.1; AT1G09700.1; AT1G09700. [O04492-1]
GeneIDi837498.
KEGGiath:AT1G09700.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF276440 mRNA. Translation: AAG49890.1.
AC000132 Genomic DNA. Translation: AAB60726.1.
CP002684 Genomic DNA. Translation: AEE28481.1.
AY054631 mRNA. Translation: AAK96822.1.
AY081525 mRNA. Translation: AAM10087.1.
AK319123 mRNA. Translation: BAH57238.1.
PIRiH86230.
RefSeqiNP_563850.1. NM_100842.3. [O04492-1]
UniGeneiAt.10223.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2L2MNMR-A97-170[»]
2L2NNMR-A1-100[»]
3ADGX-ray1.70A15-84[»]
3ADIX-ray3.20A/B/C15-84[»]
3ADJX-ray3.00A100-172[»]
ProteinModelPortaliO04492.
SMRiO04492. Positions 16-86, 100-170.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi22739. 19 interactions.
DIPiDIP-33453N.
IntActiO04492. 6 interactions.
STRINGi3702.AT1G09700.1.

PTM databases

iPTMnetiO04492.

Proteomic databases

PaxDbiO04492.
PRIDEiO04492.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G09700.1; AT1G09700.1; AT1G09700. [O04492-1]
GeneIDi837498.
KEGGiath:AT1G09700.

Organism-specific databases

TAIRiAT1G09700.

Phylogenomic databases

eggNOGiENOG410IWVA. Eukaryota.
ENOG4111ZFG. LUCA.
InParanoidiO04492.
OMAiCMNGLKE.

Miscellaneous databases

EvolutionaryTraceiO04492.
PROiO04492.

Gene expression databases

GenevisibleiO04492. AT.

Family and domain databases

Gene3Di3.30.160.20. 2 hits.
InterProiIPR014720. dsRBD_dom.
[Graphical view]
PfamiPF00035. dsrm. 2 hits.
[Graphical view]
SMARTiSM00358. DSRM. 2 hits.
[Graphical view]
PROSITEiPS50137. DS_RBD. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin."
    Lu C., Fedoroff N.
    Plant Cell 12:2351-2366(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY, INDUCTION, DISRUPTION PHENOTYPE.
    Strain: cv. No-0.
  2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
  5. "Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
    Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
    DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: cv. Columbia.
  6. "The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing."
    Vazquez F., Gasciolli V., Crete P., Vaucheret H.
    Curr. Biol. 14:346-351(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  7. "The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation."
    Han M.H., Goud S., Song L., Fedoroff N.
    Proc. Natl. Acad. Sci. U.S.A. 101:1093-1098(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  8. "Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana."
    Hiraguri A., Itoh R., Kondo N., Nomura Y., Aizawa D., Murai Y., Koiwa H., Seki M., Shinozaki K., Fukuhara T.
    Plant Mol. Biol. 57:173-188(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, INTERACTION WITH DCL1; DRB2; DRB4 AND DRB5.
  9. "SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis."
    Yang L., Liu Z., Lu F., Dong A., Huang H.
    Plant J. 47:841-850(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH SE, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
  10. "The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis."
    Kurihara Y., Takashi Y., Watanabe Y.
    RNA 12:206-212(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH DCL1.
  11. "The N-terminal double-stranded RNA binding domains of Arabidopsis HYPONASTIC LEAVES1 are sufficient for pre-microRNA processing."
    Wu F., Yu L., Cao W., Mao Y., Liu Z., He Y.
    Plant Cell 19:914-925(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, DOMAIN DSRNA-BINDING.
  12. "Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants."
    Fang Y., Spector D.L.
    Curr. Biol. 17:818-823(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  13. "The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1."
    Dong Z., Han M.-H., Fedoroff N.
    Proc. Natl. Acad. Sci. U.S.A. 105:9970-9975(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  14. Cited for: FUNCTION.
  15. "The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes."
    Eamens A.L., Smith N.A., Curtin S.J., Wang M.B., Waterhouse P.M.
    RNA 15:2219-2235(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  16. "Structure and RNA interactions of the plant MicroRNA processing-associated protein HYL1."
    Rasia R.M., Mateos J., Bologna N.G., Burdisso P., Imbert L., Palatnik J.F., Boisbouvier J.
    Biochemistry 49:8237-8239(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 1-170, FUNCTION, DOMAIN DSRNA-BINDING.
  17. "Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing."
    Yang S.W., Chen H.Y., Yang J., Machida S., Chua N.H., Yuan Y.A.
    Structure 18:594-605(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 15-172 IN COMPLEX WITH DSRNA, FUNCTION, SUBUNIT, DOMAIN DSRNA-BINDING.

Entry informationi

Entry nameiDRB1_ARATH
AccessioniPrimary (citable) accession number: O04492
Secondary accession number(s): C0Z3F9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 8, 2011
Last sequence update: July 1, 1997
Last modified: May 11, 2016
This is version 115 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Plants overexpressing HYL1 show decreased stability of transcripts targeted by miRNAs.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.