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Protein

AP2/ERF and B3 domain-containing transcription factor RAV1

Gene

RAV1

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

Functioni

Binds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3'. May function as negative regulator of plant growth and development.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi61 – 11656AP2/ERFPROSITE-ProRule annotationAdd
BLAST
DNA bindingi188 – 292105TF-B3PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: TAIR
  2. sequence-specific DNA binding transcription factor activity Source: TAIR

GO - Biological processi

  1. ethylene-activated signaling pathway Source: UniProtKB-KW
  2. lateral root development Source: TAIR
  3. leaf development Source: TAIR
  4. negative regulation of flower development Source: TAIR
  5. negative regulation of transcription, DNA-templated Source: TAIR
  6. response to brassinosteroid Source: TAIR
  7. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Ethylene signaling pathway, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
AP2/ERF and B3 domain-containing transcription factor RAV1
Alternative name(s):
Ethylene-responsive transcription factor RAV1
Protein RELATED TO ABI3/VP1 1
Gene namesi
Name:RAV1
Ordered Locus Names:At1g13260
ORF Names:T6J4.2
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G13260.

Subcellular locationi

Nucleus Curated

GO - Cellular componenti

  1. nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 344344AP2/ERF and B3 domain-containing transcription factor RAV1PRO_0000112571Add
BLAST

Proteomic databases

PRIDEiQ9ZWM9.

Expressioni

Tissue specificityi

Expressed in all tissues examined: Roots, rosette leaves, cauline leaves, inflorescence stems, flowers and siliques. Highest expression in roots and rosette leaves. Very low expression in flowers.1 Publication

Inductioni

Down-regulated by brassinosteroid and zeatin.1 Publication

Gene expression databases

GenevestigatoriQ9ZWM9.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

BioGridi23126. 5 interactions.
STRINGi3702.AT1G13260.1-P.

Structurei

Secondary structure

1
344
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi185 – 1917Combined sources
Turni194 – 1974Combined sources
Beta strandi198 – 2003Combined sources
Beta strandi203 – 2053Combined sources
Helixi207 – 2104Combined sources
Turni211 – 2133Combined sources
Beta strandi226 – 2327Combined sources
Turni233 – 2353Combined sources
Beta strandi236 – 24510Combined sources
Turni246 – 2494Combined sources
Beta strandi250 – 2567Combined sources
Helixi257 – 2637Combined sources
Beta strandi271 – 2766Combined sources
Beta strandi279 – 2813Combined sources
Beta strandi284 – 2896Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WIDNMR-A182-298[»]
ProteinModelPortaliQ9ZWM9.
SMRiQ9ZWM9. Positions 62-115, 182-298.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9ZWM9.

Family & Domainsi

Domaini

Contains two distinct DNA-binding domains. One is located in the N-terminal region and binds to the 5'-CAACA-3' motif. The second is located in the C-terminal region and binds to the 5'-CACCTG-3' motif.

Sequence similaritiesi

Contains 1 AP2/ERF DNA-binding domain.PROSITE-ProRule annotation
Contains 1 TF-B3 DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG266118.
HOGENOMiHOG000237484.
KOiK09287.
OMAiICETPAI.
PhylomeDBiQ9ZWM9.

Family and domain databases

Gene3Di2.40.330.10. 1 hit.
3.30.730.10. 1 hit.
InterProiIPR001471. AP2/ERF_dom.
IPR003340. B3_DNA-bd.
IPR016177. DNA-bd_dom.
IPR015300. DNA-bd_pseudobarrel.
[Graphical view]
PfamiPF00847. AP2. 1 hit.
PF02362. B3. 1 hit.
[Graphical view]
SMARTiSM00380. AP2. 1 hit.
SM01019. B3. 1 hit.
[Graphical view]
SUPFAMiSSF101936. SSF101936. 1 hit.
SSF54171. SSF54171. 1 hit.
PROSITEiPS51032. AP2_ERF. 1 hit.
PS50863. B3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9ZWM9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MESSSVDEST TSTGSICETP AITPAKKSSV GNLYRMGSGS SVVLDSENGV
60 70 80 90 100
EAESRKLPSS KYKGVVPQPN GRWGAQIYEK HQRVWLGTFN EEDEAARAYD
110 120 130 140 150
VAVHRFRRRD AVTNFKDVKM DEDEVDFLNS HSKSEIVDML RKHTYNEELE
160 170 180 190 200
QSKRRRNGNG NMTRTLLTSG LSNDGVSTTG FRSAEALFEK AVTPSDVGKL
210 220 230 240 250
NRLVIPKHHA EKHFPLPSSN VSVKGVLLNF EDVNGKVWRF RYSYWNSSQS
260 270 280 290 300
YVLTKGWSRF VKEKNLRAGD VVSFSRSNGQ DQQLYIGWKS RSGSDLDAGR
310 320 330 340
VLRLFGVNIS PESSRNDVVG NKRVNDTEML SLVCSKKQRI FHAS
Length:344
Mass (Da):38,597
Last modified:April 30, 1999 - v1
Checksum:i7349B640B3505823
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB013886 mRNA. Translation: BAA34250.1.
AC011810 Genomic DNA. Translation: AAG09554.1.
CP002684 Genomic DNA. Translation: AEE28991.1.
AY063855 mRNA. Translation: AAL36211.1.
AY091291 mRNA. Translation: AAM14230.1.
PIRiT51329.
RefSeqiNP_172784.1. NM_101197.3.
UniGeneiAt.20558.

Genome annotation databases

EnsemblPlantsiAT1G13260.1; AT1G13260.1; AT1G13260.
GeneIDi837886.
KEGGiath:AT1G13260.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB013886 mRNA. Translation: BAA34250.1.
AC011810 Genomic DNA. Translation: AAG09554.1.
CP002684 Genomic DNA. Translation: AEE28991.1.
AY063855 mRNA. Translation: AAL36211.1.
AY091291 mRNA. Translation: AAM14230.1.
PIRiT51329.
RefSeqiNP_172784.1. NM_101197.3.
UniGeneiAt.20558.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WIDNMR-A182-298[»]
ProteinModelPortaliQ9ZWM9.
SMRiQ9ZWM9. Positions 62-115, 182-298.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi23126. 5 interactions.
STRINGi3702.AT1G13260.1-P.

Proteomic databases

PRIDEiQ9ZWM9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G13260.1; AT1G13260.1; AT1G13260.
GeneIDi837886.
KEGGiath:AT1G13260.

Organism-specific databases

TAIRiAT1G13260.

Phylogenomic databases

eggNOGiNOG266118.
HOGENOMiHOG000237484.
KOiK09287.
OMAiICETPAI.
PhylomeDBiQ9ZWM9.

Miscellaneous databases

EvolutionaryTraceiQ9ZWM9.

Gene expression databases

GenevestigatoriQ9ZWM9.

Family and domain databases

Gene3Di2.40.330.10. 1 hit.
3.30.730.10. 1 hit.
InterProiIPR001471. AP2/ERF_dom.
IPR003340. B3_DNA-bd.
IPR016177. DNA-bd_dom.
IPR015300. DNA-bd_pseudobarrel.
[Graphical view]
PfamiPF00847. AP2. 1 hit.
PF02362. B3. 1 hit.
[Graphical view]
SMARTiSM00380. AP2. 1 hit.
SM01019. B3. 1 hit.
[Graphical view]
SUPFAMiSSF101936. SSF101936. 1 hit.
SSF54171. SSF54171. 1 hit.
PROSITEiPS51032. AP2_ERF. 1 hit.
PS50863. B3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants."
    Kagaya Y., Ohmiya K., Hattori T.
    Nucleic Acids Res. 27:470-478(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY.
    Strain: cv. Columbia.
    Tissue: Seedling.
  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(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-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(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. Cited for: GENE FAMILY.
  6. "Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1."
    Yamasaki K., Kigawa T., Inoue M., Tateno M., Yamasaki T., Yabuki T., Aoki M., Seki E., Matsuda T., Tomo Y., Hayami N., Terada T., Shirouzu M., Osanai T., Tanaka A., Seki M., Shinozaki K., Yokoyama S.
    Plant Cell 16:3448-3459(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 182-298.
  7. "Genome-wide analysis of the ERF gene family in Arabidopsis and rice."
    Nakano T., Suzuki K., Fujimura T., Shinshi H.
    Plant Physiol. 140:411-432(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.
  8. "Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development."
    Hu Y.X., Wang Y.H., Liu X.F., Li J.Y.
    Cell Res. 14:8-15(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION.

Entry informationi

Entry nameiRAV1_ARATH
AccessioniPrimary (citable) accession number: Q9ZWM9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 14, 2002
Last sequence update: April 30, 1999
Last modified: January 6, 2015
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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

External Data

Dasty 3

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 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.