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Protein

Tudor domain-containing protein 3

Gene

TDRD3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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
  • poly(A) RNA binding Source: UniProtKB
  • transcription coactivator activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Enzyme and pathway databases

BioCyciZFISH:ENSG00000083544-MONOMER.

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

HGNCiHGNC:20612. TDRD3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
Complete GO annotation...

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.

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

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ9H7E2.
PaxDbiQ9H7E2.
PeptideAtlasiQ9H7E2.
PRIDEiQ9H7E2.

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.

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

GO - Molecular functioni

  • methylated histone binding Source: UniProtKB

Protein-protein interaction databases

BioGridi123514. 32 interactors.
DIPiDIP-61935N.
IntActiQ9H7E2. 12 interactors.
STRINGi9606.ENSP00000440190.

Structurei

Secondary structure

1651
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi196 – 203Combined sources8
Turni204 – 206Combined sources3
Helixi209 – 218Combined sources10
Helixi223 – 233Combined sources11
Helixi550 – 553Combined sources4
Beta strandi561 – 566Combined sources6
Turni567 – 570Combined sources4
Beta strandi571 – 579Combined sources9
Beta strandi585 – 591Combined sources7
Turni592 – 594Combined sources3
Beta strandi597 – 601Combined sources5
Helixi602 – 604Combined sources3
Beta strandi605 – 607Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WJINMR-A194-243[»]
2LTONMR-A554-608[»]
3PMTX-ray1.80A553-611[»]
3PNWX-ray2.05C/F/I/L/O/R/U/X540-615[»]
3S6WX-ray1.78A555-608[»]
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

Sequence similaritiesi

Contains 1 Tudor domain.PROSITE-ProRule annotation
Contains 1 UBA domain.PROSITE-ProRule annotation

Phylogenomic databases

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

Family and domain databases

InterProiIPR013894. RMI1_N.
IPR002999. Tudor.
IPR015940. UBA.
IPR009060. UBA-like.
[Graphical view]
PfamiPF08585. RMI1_N. 1 hit.
PF00567. TUDOR. 1 hit.
PF00627. UBA. 1 hit.
[Graphical view]
SMARTiSM00333. TUDOR. 1 hit.
SM00165. UBA. 1 hit.
[Graphical view]
SUPFAMiSSF46934. SSF46934. 1 hit.
PROSITEiPS50304. TUDOR. 1 hit.
PS50030. UBA. 1 hit.
[Graphical view]

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, AL512666 Genomic DNA. Translation: CAH72281.1.
AL512666, AL354764 Genomic DNA. Translation: CAH74000.1.
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

Cross-referencesi

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, AL512666 Genomic DNA. Translation: CAH72281.1.
AL512666, AL354764 Genomic DNA. Translation: CAH74000.1.
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WJINMR-A194-243[»]
2LTONMR-A554-608[»]
3PMTX-ray1.80A553-611[»]
3PNWX-ray2.05C/F/I/L/O/R/U/X540-615[»]
3S6WX-ray1.78A555-608[»]
ProteinModelPortaliQ9H7E2.
SMRiQ9H7E2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123514. 32 interactors.
DIPiDIP-61935N.
IntActiQ9H7E2. 12 interactors.
STRINGi9606.ENSP00000440190.

PTM databases

iPTMnetiQ9H7E2.
PhosphoSitePlusiQ9H7E2.

Polymorphism and mutation databases

BioMutaiTDRD3.
DMDMi29337133.

Proteomic databases

MaxQBiQ9H7E2.
PaxDbiQ9H7E2.
PeptideAtlasiQ9H7E2.
PRIDEiQ9H7E2.

Protocols and materials databases

DNASUi81550.
Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi81550.
DisGeNETi81550.
GeneCardsiTDRD3.
HGNCiHGNC:20612. TDRD3.
HPAiCAB034925.
MIMi614392. gene.
neXtProtiNX_Q9H7E2.
OpenTargetsiENSG00000083544.
PharmGKBiPA134962690.
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

BioCyciZFISH:ENSG00000083544-MONOMER.

Miscellaneous databases

ChiTaRSiTDRD3. human.
EvolutionaryTraceiQ9H7E2.
GeneWikiiTDRD3.
GenomeRNAii81550.
PROiQ9H7E2.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000083544.
CleanExiHS_TDRD3.
ExpressionAtlasiQ9H7E2. baseline and differential.
GenevisibleiQ9H7E2. HS.

Family and domain databases

InterProiIPR013894. RMI1_N.
IPR002999. Tudor.
IPR015940. UBA.
IPR009060. UBA-like.
[Graphical view]
PfamiPF08585. RMI1_N. 1 hit.
PF00567. TUDOR. 1 hit.
PF00627. UBA. 1 hit.
[Graphical view]
SMARTiSM00333. TUDOR. 1 hit.
SM00165. UBA. 1 hit.
[Graphical view]
SUPFAMiSSF46934. SSF46934. 1 hit.
PROSITEiPS50304. TUDOR. 1 hit.
PS50030. UBA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTDRD3_HUMAN
AccessioniPrimary (citable) accession number: Q9H7E2
Secondary accession number(s): B2MWP9, Q53XA6, Q6P992
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: March 1, 2001
Last modified: November 2, 2016
This is version 127 of the entry and version 1 of the sequence. [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
  4. 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.