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Protein

Tudor domain-containing protein 3

Gene

TDRD3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins.3 Publications

GO - Molecular functioni

  • chromatin binding Source: UniProtKB
  • methylated histone binding Source: UniProtKB
  • RNA binding Source: UniProtKB
  • transcription coactivator activity Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator

Enzyme and pathway databases

SIGNORiQ9H7E2

Names & Taxonomyi

Protein namesi
Recommended name:
Tudor domain-containing protein 3
Gene namesi
Name:TDRD3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 13

Organism-specific databases

EuPathDBiHostDB:ENSG00000083544.13
HGNCiHGNC:20612 TDRD3
MIMi614392 gene
neXtProtiNX_Q9H7E2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi598E → K: Abolishes interaction with dimethylarginine-containing protein motifs and reduces association with mRNA stress granules. 1 Publication1
Mutagenesisi638 – 644RPTQQFY → EPTQQFE: Loss of interaction with the EJC. 1 Publication7

Organism-specific databases

DisGeNETi81550
OpenTargetsiENSG00000083544
PharmGKBiPA134962690

Chemistry databases

ChEMBLiCHEMBL3879852

Polymorphism and mutation databases

BioMutaiTDRD3
DMDMi29337133

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001831631 – 651Tudor domain-containing protein 3Add BLAST651

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei256PhosphoserineCombined sources1
Modified residuei345PhosphoserineCombined sources1
Cross-linki470Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ9H7E2
PaxDbiQ9H7E2
PeptideAtlasiQ9H7E2
PRIDEiQ9H7E2
ProteomicsDBi81113
81114 [Q9H7E2-2]
81115 [Q9H7E2-3]

PTM databases

iPTMnetiQ9H7E2
PhosphoSitePlusiQ9H7E2

Expressioni

Tissue specificityi

Detected in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas.1 Publication

Gene expression databases

BgeeiENSG00000083544
CleanExiHS_TDRD3
ExpressionAtlasiQ9H7E2 baseline and differential
GenevisibleiQ9H7E2 HS

Organism-specific databases

HPAiCAB034925
HPA067153

Interactioni

Subunit structurei

Component of mRNA stress granules. Interacts with FMR1, FXR1, FXR2, EWSR1, FUS, SERBP1, EEF1A1 and DDX3X or DDX3Y, and with the small nuclear ribonucleoprotein-associated proteins SNRPB and SNRPN. Interacts with 'Lys-48'-linked tetra-ubiquitin, but not with monoubiquitin or 'Lys-63'-linked ubiquitin chains. May interact with the exon junction complex (EJC) composed at least of CASC3, EIF4A3, MAGOH and RBM8A. Interacts with POLR2A (via the C-terminal domain (CTD)).5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
POLR2AP249283EBI-3938232,EBI-295301

GO - Molecular functioni

  • methylated histone binding Source: UniProtKB

Protein-protein interaction databases

BioGridi123514, 34 interactors
ComplexPortaliCPX-1621 TDRD3-TOP3B type IA topoisomerase complex [Q9H7E2-3]
DIPiDIP-61935N
IntActiQ9H7E2, 15 interactors
STRINGi9606.ENSP00000440190

Structurei

Secondary structure

1651
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 21Combined sources21
Beta strandi33 – 36Combined sources4
Beta strandi38 – 43Combined sources6
Beta strandi46 – 50Combined sources5
Turni51 – 53Combined sources3
Beta strandi54 – 58Combined sources5
Helixi196 – 203Combined sources8
Turni204 – 206Combined sources3
Helixi209 – 218Combined sources10
Helixi223 – 233Combined sources11
Helixi550 – 553Combined sources4
Beta strandi561 – 565Combined sources5
Turni567 – 569Combined sources3
Beta strandi572 – 581Combined sources10
Turni582 – 585Combined sources4
Beta strandi586 – 591Combined sources6
Turni592 – 594Combined sources3
Beta strandi597 – 601Combined sources5
Helixi602 – 604Combined sources3
Beta strandi605 – 607Combined sources3

3D structure databases

ProteinModelPortaliQ9H7E2
SMRiQ9H7E2
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H7E2

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini193 – 233UBAPROSITE-ProRule annotationAdd BLAST41
Domaini555 – 615TudorPROSITE-ProRule annotationAdd BLAST61

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni631 – 651EBM motif; may mediate interaction with the EJCAdd BLAST21

Domaini

The Tudor domain specifically recognizes and binds asymmetric dimethylation of histone H3 'Arg-17' (H3R17me2a) and histones H4 'Arg-3', 2 tags for epigenetic transcriptional activation.1 Publication

Phylogenomic databases

eggNOGiKOG3683 Eukaryota
ENOG4111KPK LUCA
GeneTreeiENSGT00740000115530
HOGENOMiHOG000154539
HOVERGENiHBG059153
InParanoidiQ9H7E2
KOiK18404
OMAiCDRPYSR
OrthoDBiEOG091G0GU8
PhylomeDBiQ9H7E2
TreeFamiTF316491

Family and domain databases

InterProiView protein in InterPro
IPR013894 RMI1_N
IPR002999 Tudor
IPR015940 UBA
IPR009060 UBA-like_sf
PfamiView protein in Pfam
PF08585 RMI1_N, 1 hit
PF00567 TUDOR, 1 hit
PF00627 UBA, 1 hit
SMARTiView protein in SMART
SM00333 TUDOR, 1 hit
SM00165 UBA, 1 hit
SUPFAMiSSF46934 SSF46934, 1 hit
PROSITEiView protein in PROSITE
PS50304 TUDOR, 1 hit
PS50030 UBA, 1 hit

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9H7E2-1) [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
MLRLQMTDGH ISCTAVEFSY MSKISLNTPP GTKVKLSGIV DIKNGFLLLN
60 70 80 90 100
DSNTTVLGGE VEHLIEKWEL QRSLSKHNRS NIGTEGGPPP FVPFGQKCVS
110 120 130 140 150
HVQVDSRELD RRKTLQVTMP VKPTNDNDEF EKQRTAAIAE VAKSKETKTF
160 170 180 190 200
GGGGGGARSN LNMNAAGNRN REVLQKEKST KSEGKHEGVY RELVDEKALK
210 220 230 240 250
HITEMGFSKE ASRQALMDNG NNLEAALNVL LTSNKQKPVM GPPLRGRGKG
260 270 280 290 300
RGRIRSEDEE DLGNARPSAP STLFDFLESK MGTLNVEEPK SQPQQLHQGQ
310 320 330 340 350
YRSSNTEQNG VKDNNHLRHP PRNDTRQPRN EKPPRFQRDS QNSKSVLEGS
360 370 380 390 400
GLPRNRGSER PSTSSVSEVW AEDRIKCDRP YSRYDRTKDT SYPLGSQHSD
410 420 430 440 450
GAFKKRDNSM QSRSGKGPSF AEAKENPLPQ GSVDYNNQKR GKRESQTSIP
460 470 480 490 500
DYFYDRKSQT INNEAFSGIK IEKHFNVNTD YQNPVRSNSF IGVPNGEVEM
510 520 530 540 550
PLKGRRIGPI KPAGPVTAVP CDDKIFYNSG PKRRSGPIKP EKILESSIPM
560 570 580 590 600
EYAKMWKPGD ECFALYWEDN KFYRAEVEAL HSSGMTAVVK FIDYGNYEEV
610 620 630 640 650
LLSNIKPIQT EAWEEEGTYD QTLEFRRGGD GQPRRSTRPT QQFYQPPRAR

N
Length:651
Mass (Da):73,185
Last modified:March 1, 2001 - v1
Checksum:i1D82F323F6EF4B05
GO
Isoform 2 (identifier: Q9H7E2-2) [UniParc]FASTAAdd to basket
Also known as: Long

The sequence of this isoform differs from the canonical sequence as follows:
     97-97: Missing.

Show »
Length:650
Mass (Da):73,057
Checksum:i997FB4382F678469
GO
Isoform 3 (identifier: Q9H7E2-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MAQVAGAALS...NEESQAAPRM

Show »
Length:744
Mass (Da):83,103
Checksum:iCF27720025EFBD81
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti101H → R in AAH60876 (PubMed:15489334).Curated1
Sequence conflicti509P → H in AAH60876 (PubMed:15489334).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0370521M → MAQVAGAALSQAGWYLSDEG IEACTSSPDKVNVNDIILIA LNTDLRTIGKKFLPSDINSG KVEKLEGPCVLQIQKIRNVA APKDNEESQAAPRM in isoform 3. 1 Publication1
Alternative sequenceiVSP_03705397Missing in isoform 2. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU643838 mRNA Translation: ACC94142.1
AK024660 mRNA Translation: BAB14950.1
BX537910 mRNA Translation: CAD97894.1
AL354764 Genomic DNA No translation available.
AL512666 Genomic DNA No translation available.
CH471124 Genomic DNA Translation: EAW52079.1
BC030514 mRNA Translation: AAH30514.1
BC060876 mRNA Translation: AAH60876.1
CCDSiCCDS53872.1 [Q9H7E2-3]
CCDS9441.1 [Q9H7E2-1]
RefSeqiNP_001139542.1, NM_001146070.1 [Q9H7E2-3]
NP_001139543.1, NM_001146071.1 [Q9H7E2-1]
NP_110421.1, NM_030794.2 [Q9H7E2-1]
XP_016876266.1, XM_017020777.1 [Q9H7E2-3]
UniGeneiHs.525061

Genome annotation databases

EnsembliENST00000196169; ENSP00000196169; ENSG00000083544 [Q9H7E2-1]
ENST00000377881; ENSP00000367113; ENSG00000083544 [Q9H7E2-1]
ENST00000377894; ENSP00000367126; ENSG00000083544 [Q9H7E2-1]
ENST00000535286; ENSP00000440190; ENSG00000083544 [Q9H7E2-3]
ENST00000621840; ENSP00000477993; ENSG00000083544 [Q9H7E2-2]
GeneIDi81550
KEGGihsa:81550
UCSCiuc001vhz.5 human [Q9H7E2-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiTDRD3_HUMAN
AccessioniPrimary (citable) accession number: Q9H7E2
Secondary accession number(s): B2MWP9, Q53XA6, Q6P992
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: March 1, 2001
Last modified: July 18, 2018
This is version 140 of the entry and version 1 of the sequence. See 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 13
    Human chromosome 13: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

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