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Protein

Protein RDM1

Gene

RDM1

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

Functioni

Regulator of RNA-directed DNA methylation (RdDM). Binds to single-stranded methyl DNA. Involved in the assembly of RNA polymerase V (Pol V) transcription initiation or elongation complexes at the chromatin, as a component of the DDR complex.3 Publications

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • protein self-association Source: UniProtKB

GO - Biological processi

  • DNA methylation Source: TAIR
  • production of small RNA involved in gene silencing by RNA Source: UniProtKB
  • regulation of DNA methylation Source: UniProtKB
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Protein RDM1
Alternative name(s):
Protein RNA-directed DNA methylation 1
Gene namesi
Name:RDM1
Ordered Locus Names:At3g22680
ORF Names:MWI23.5
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G22680.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase V complex Source: UniProtKB
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Impaired accumulation of siRNAs, reduced DNA methylation, and loss of transcriptional gene silencing at RdDM target loci. Impaired RNA polymerase V-chromatin associations (Pol V).3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi50M → A: Decreased binding to single-stranded methyl DNA. 1 Publication1
Mutagenesisi152 – 163Missing in rdm1-1; reduced DNA methylation. 1 PublicationAdd BLAST12

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002206051 – 163Protein RDM1Add BLAST163

Proteomic databases

PaxDbiQ9LUJ3.

Expressioni

Gene expression databases

GenevisibleiQ9LUJ3. AT.

Interactioni

Subunit structurei

Homodimer. Interacts with AGO4, RPB205 and DRM2. Part of the chromatin-remodeling complex (DDR complex) that contains at least DRD1, DMS3 and RDM1. The DDR complex recruits/activates the RNA polymerases V acts duing siRNA-directed DNA methylation (RdDM).2 Publications

GO - Molecular functioni

  • protein self-association Source: UniProtKB

Protein-protein interaction databases

BioGridi7171. 6 interactors.
DIPiDIP-59278N.
STRINGi3702.AT3G22680.1.

Structurei

Secondary structure

1163
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi45 – 56Combined sources12
Helixi73 – 84Combined sources12
Helixi90 – 101Combined sources12
Turni102 – 105Combined sources4
Helixi113 – 115Combined sources3
Helixi119 – 135Combined sources17
Helixi139 – 148Combined sources10
Helixi152 – 155Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VK5X-ray1.60A8-163[»]
2Q3TX-ray1.60A8-163[»]
3GANX-ray2.00A8-163[»]
ProteinModelPortaliQ9LUJ3.
SMRiQ9LUJ3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9LUJ3.

Family & Domainsi

Phylogenomic databases

eggNOGiENOG410IYJS. Eukaryota.
ENOG410XVRY. LUCA.
HOGENOMiHOG000090795.
InParanoidiQ9LUJ3.
OMAiSDPMYHS.
OrthoDBiEOG09360Q3D.
PhylomeDBiQ9LUJ3.

Family and domain databases

InterProiIPR015270. RDM1.
[Graphical view]
PfamiPF09187. DUF1950. 1 hit.
[Graphical view]
SUPFAMiSSF109920. SSF109920. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9LUJ3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQSSMTMELR PSGDSGSSDV DAEISDGFSP LDTSHRDVAD EGSLLRRAEM
60 70 80 90 100
YQDYMKQVPI PTNRGSLIPF TSWVGLSISM KQLYGQPLHY LTNVLLQRWD
110 120 130 140 150
QSRFGTDSEE QRLDSIIHPT KAEATIWLVE EIHRLTPSHL HMALLWRSDP
160
MYHSFIDPIF PEK
Length:163
Mass (Da):18,692
Last modified:October 1, 2000 - v1
Checksum:i824051FDD1F11DFB
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti121K → S in AAP21198 (PubMed:14593172).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB022223 Genomic DNA. Translation: BAB01243.1.
CP002686 Genomic DNA. Translation: AEE76664.1.
BT006390 mRNA. Translation: AAP21198.1.
RefSeqiNP_188907.2. NM_113167.5.
UniGeneiAt.6299.

Genome annotation databases

EnsemblPlantsiAT3G22680.1; AT3G22680.1; AT3G22680.
GeneIDi821839.
GrameneiAT3G22680.1; AT3G22680.1; AT3G22680.
KEGGiath:AT3G22680.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB022223 Genomic DNA. Translation: BAB01243.1.
CP002686 Genomic DNA. Translation: AEE76664.1.
BT006390 mRNA. Translation: AAP21198.1.
RefSeqiNP_188907.2. NM_113167.5.
UniGeneiAt.6299.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VK5X-ray1.60A8-163[»]
2Q3TX-ray1.60A8-163[»]
3GANX-ray2.00A8-163[»]
ProteinModelPortaliQ9LUJ3.
SMRiQ9LUJ3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi7171. 6 interactors.
DIPiDIP-59278N.
STRINGi3702.AT3G22680.1.

Proteomic databases

PaxDbiQ9LUJ3.

Protocols and materials databases

DNASUi821839.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G22680.1; AT3G22680.1; AT3G22680.
GeneIDi821839.
GrameneiAT3G22680.1; AT3G22680.1; AT3G22680.
KEGGiath:AT3G22680.

Organism-specific databases

TAIRiAT3G22680.

Phylogenomic databases

eggNOGiENOG410IYJS. Eukaryota.
ENOG410XVRY. LUCA.
HOGENOMiHOG000090795.
InParanoidiQ9LUJ3.
OMAiSDPMYHS.
OrthoDBiEOG09360Q3D.
PhylomeDBiQ9LUJ3.

Miscellaneous databases

EvolutionaryTraceiQ9LUJ3.
PROiQ9LUJ3.

Gene expression databases

GenevisibleiQ9LUJ3. AT.

Family and domain databases

InterProiIPR015270. RDM1.
[Graphical view]
PfamiPF09187. DUF1950. 1 hit.
[Graphical view]
SUPFAMiSSF109920. SSF109920. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRDM1_ARATH
AccessioniPrimary (citable) accession number: Q9LUJ3
Secondary accession number(s): Q84MD0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: October 1, 2000
Last modified: November 30, 2016
This is version 97 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

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.