UniProtKB - Q39212 (RPD3B_ARATH)
Protein
DNA-directed RNA polymerases IV and V subunit 3B
Gene
NRPD3B
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Functioni
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerases IV and V which mediate short-interfering RNAs (siRNA) accumulation and subsequent RNA-directed DNA methylation-dependent (RdDM) transcriptional gene silencing (TGS) of endogenous repeated sequences, including transposable elements.1 Publication
GO - Molecular functioni
- DNA binding Source: InterPro
- DNA-directed 5'-3' RNA polymerase activity Source: UniProtKB-KW
- protein dimerization activity Source: InterPro
GO - Biological processi
- transcription, DNA-templated Source: InterPro
Keywordsi
Biological process | Transcription |
Names & Taxonomyi
Protein namesi | Recommended name: DNA-directed RNA polymerases IV and V subunit 3BAlternative name(s): DNA-directed RNA polymerase II 36 kDa polypeptide B DNA-directed RNA polymerase II subunit RPB3-B Short name: RNA polymerase II subunit 3-B Short name: RNA polymerase II subunit B3-B |
Gene namesi | Name:NRPD3B Synonyms:NRPE3B, RPB36B Ordered Locus Names:At2g15400 ORF Names:F26H6.8 |
Organismi | Arabidopsis thaliana (Mouse-ear cress) |
Taxonomic identifieri | 3702 [NCBI] |
Taxonomic lineagei | Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliopsida › eudicotyledons › Gunneridae › Pentapetalae › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis |
Proteomesi |
|
Organism-specific databases
Araporti | AT2G15400 |
TAIRi | locus:2047198, AT2G15400 |
Subcellular locationi
Nucleus
- Nucleus By similarity
Nucleus
- RNA polymerase II, core complex Source: GO_Central
- RNA polymerase IV complex Source: UniProtKB
- RNA polymerase V complex Source: UniProtKB
Keywords - Cellular componenti
DNA-directed RNA polymerase, NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000132746 | 1 – 319 | DNA-directed RNA polymerases IV and V subunit 3BAdd BLAST | 319 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 1 | N-acetylmethionineBy similarity | 1 |
Keywords - PTMi
AcetylationProteomic databases
PaxDbi | Q39212 |
PRIDEi | Q39212 |
ProteomicsDBi | 228231 [Q39212-1] |
Expressioni
Gene expression databases
ExpressionAtlasi | Q39212, baseline and differential |
Genevisiblei | Q39212, AT |
Interactioni
Subunit structurei
Component of the RNA polymerase IV and V complexes.
Interacts with NRPB11, SHH1, GRP23 and NRPD1.
5 PublicationsBinary interactionsi
Q39212
With | #Exp. | IntAct |
---|---|---|
GRP23 [Q9SY69] | 3 | EBI-1769627,EBI-1769617 |
GO - Molecular functioni
- protein dimerization activity Source: InterPro
Protein-protein interaction databases
BioGRIDi | 1391, 8 interactors |
IntActi | Q39212, 1 interactor |
STRINGi | 3702.AT2G15400.1 |
Family & Domainsi
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 230 – 233 | Poly-Val | 4 |
Sequence similaritiesi
Belongs to the archaeal RpoD/eukaryotic RPB3 RNA polymerase subunit family.Curated
Phylogenomic databases
eggNOGi | KOG1522, Eukaryota |
HOGENOMi | CLU_038421_3_0_1 |
InParanoidi | Q39212 |
OMAi | HDSFVFT |
PhylomeDBi | Q39212 |
Family and domain databases
Gene3Di | 2.170.120.12, 1 hit |
InterProi | View protein in InterPro IPR001514, DNA-dir_RNA_pol_30-40kDasu_CS IPR011262, DNA-dir_RNA_pol_insert IPR011263, DNA-dir_RNA_pol_RpoA/D/Rpb3 IPR036603, RBP11-like IPR036643, RNApol_insert_sf |
Pfami | View protein in Pfam PF01000, RNA_pol_A_bac, 1 hit PF01193, RNA_pol_L, 1 hit |
SMARTi | View protein in SMART SM00662, RPOLD, 1 hit |
SUPFAMi | SSF55257, SSF55257, 1 hit SSF56553, SSF56553, 1 hit |
PROSITEi | View protein in PROSITE PS00446, RNA_POL_D_30KD, 1 hit |
(1+)i Sequence
Sequence statusi: Complete.
This entry describes 1 produced by isoform ialternative splicing. AlignAdd to basketNote: A number of isoforms are produced. According to EST sequences.
This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All
Isoform 1 (identifier: Q39212-1) [UniParc]FASTAAdd to basket
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MDGVTYQRFP TVKIRELKDD YAKFELRETD VSMANALRRV MISEVPTMAI
60 70 80 90 100
HLVKIEVNSS VLNDEFIAQR LSLIPLTSER AMSMRFCQDC EDCNGDEHCE
110 120 130 140 150
FCSVEFPLSA KCVTDQTLDV TSRDLYSADP TVTPVDFTSN SSTSDSSEHK
160 170 180 190 200
GIIIAKLRRG QELKLKALAR KGIGKDHAKW SPAATVTYMY EPDIIINEEM
210 220 230 240 250
MNTLTDEEKI DLIESSPTKV FGIDPVTGQV VVVDPEAYTY DEEVIKKAEA
260 270 280 290 300
MGKPGLIEIH PKHDSFVFTV ESTGALKASQ LVLNAIDILK QKLDAIRLSD
310
NTVEADDQFG ELGAHMREG
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketA8MR04 | A8MR04_ARATH | DNA-directed RNA polymerase family ... | NRPE3B RBP36B, At2g15400, F26H6.8, F26H6_8 | 235 | Annotation score: |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 268 – 271 | FTVE → LSVH in AAB03740 (PubMed:8617787).Curated | 4 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L34771 Genomic DNA Translation: AAB03740.1 AC006920 Genomic DNA Translation: AAD22284.1 CP002685 Genomic DNA Translation: AEC06397.1 BT005715 mRNA Translation: AAO64135.1 BT006072 mRNA Translation: AAP04057.1 |
PIRi | E84528 S71177 |
RefSeqi | NP_179142.1, NM_127100.4 [Q39212-1] |
Genome annotation databases
EnsemblPlantsi | AT2G15400.1; AT2G15400.1; AT2G15400 [Q39212-1] |
GeneIDi | 816032 |
Gramenei | AT2G15400.1; AT2G15400.1; AT2G15400 [Q39212-1] |
KEGGi | ath:AT2G15400 |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L34771 Genomic DNA Translation: AAB03740.1 AC006920 Genomic DNA Translation: AAD22284.1 CP002685 Genomic DNA Translation: AEC06397.1 BT005715 mRNA Translation: AAO64135.1 BT006072 mRNA Translation: AAP04057.1 |
PIRi | E84528 S71177 |
RefSeqi | NP_179142.1, NM_127100.4 [Q39212-1] |
3D structure databases
SMRi | Q39212 |
ModBasei | Search... |
Protein-protein interaction databases
BioGRIDi | 1391, 8 interactors |
IntActi | Q39212, 1 interactor |
STRINGi | 3702.AT2G15400.1 |
Proteomic databases
PaxDbi | Q39212 |
PRIDEi | Q39212 |
ProteomicsDBi | 228231 [Q39212-1] |
Genome annotation databases
EnsemblPlantsi | AT2G15400.1; AT2G15400.1; AT2G15400 [Q39212-1] |
GeneIDi | 816032 |
Gramenei | AT2G15400.1; AT2G15400.1; AT2G15400 [Q39212-1] |
KEGGi | ath:AT2G15400 |
Organism-specific databases
Araporti | AT2G15400 |
TAIRi | locus:2047198, AT2G15400 |
Phylogenomic databases
eggNOGi | KOG1522, Eukaryota |
HOGENOMi | CLU_038421_3_0_1 |
InParanoidi | Q39212 |
OMAi | HDSFVFT |
PhylomeDBi | Q39212 |
Miscellaneous databases
PROi | PR:Q39212 |
Gene expression databases
ExpressionAtlasi | Q39212, baseline and differential |
Genevisiblei | Q39212, AT |
Family and domain databases
Gene3Di | 2.170.120.12, 1 hit |
InterProi | View protein in InterPro IPR001514, DNA-dir_RNA_pol_30-40kDasu_CS IPR011262, DNA-dir_RNA_pol_insert IPR011263, DNA-dir_RNA_pol_RpoA/D/Rpb3 IPR036603, RBP11-like IPR036643, RNApol_insert_sf |
Pfami | View protein in Pfam PF01000, RNA_pol_A_bac, 1 hit PF01193, RNA_pol_L, 1 hit |
SMARTi | View protein in SMART SM00662, RPOLD, 1 hit |
SUPFAMi | SSF55257, SSF55257, 1 hit SSF56553, SSF56553, 1 hit |
PROSITEi | View protein in PROSITE PS00446, RNA_POL_D_30KD, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | RPD3B_ARATH | |
Accessioni | Q39212Primary (citable) accession number: Q39212 Secondary accession number(s): Q9SJP1 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | December 1, 2000 |
Last sequence update: | December 1, 2000 | |
Last modified: | December 2, 2020 | |
This is version 167 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Plant Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- Arabidopsis thaliana
Arabidopsis thaliana: entries and gene names - SIMILARITY comments
Index of protein domains and families