Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q9H7E2 (TDRD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 104. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Tudor domain-containing protein 3
Gene names
Name:TDRD3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length651 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.7 Ref.12

Subunit structure

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. Ref.1 Ref.7 Ref.8 Ref.11

Subcellular location

Cytoplasm. Nucleus. Note: Predominantly cytoplasmic. Associated with actively translating polyribosomes and with mRNA stress granules. Ref.1 Ref.8 Ref.12

Tissue specificity

Detected in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Ref.8

Domain

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. Ref.12

Sequence similarities

Contains 1 Tudor domain.

Contains 1 UBA domain.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9H7E2-1)

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.
Isoform 2 (identifier: Q9H7E2-2)

Also known as: Long;

The sequence of this isoform differs from the canonical sequence as follows:
     97-97: Missing.
Isoform 3 (identifier: Q9H7E2-3)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 651651Tudor domain-containing protein 3
PRO_0000183163

Regions

Domain193 – 23341UBA
Domain555 – 61561Tudor
Region631 – 65121EBM motif; may mediate interaction with the EJC

Amino acid modifications

Modified residue2561Phosphoserine Ref.9 Ref.10

Natural variations

Alternative sequence11M → MAQVAGAALSQAGWYLSDEG IEACTSSPDKVNVNDIILIA LNTDLRTIGKKFLPSDINSG KVEKLEGPCVLQIQKIRNVA APKDNEESQAAPRM in isoform 3.
VSP_037052
Alternative sequence971Missing in isoform 2.
VSP_037053

Experimental info

Mutagenesis5981E → K: Abolishes interaction with dimethylarginine-containing protein motifs and reduces association with mRNA stress granules. Ref.1
Mutagenesis638 – 6447RPTQQFY → EPTQQFE: Loss of interaction with the EJC. Ref.11
Sequence conflict1011H → R in AAH60876. Ref.6
Sequence conflict5091P → H in AAH60876. Ref.6

Secondary structure

..................... 651
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: 1D82F323F6EF4B05

FASTA65173,185
        10         20         30         40         50         60 
MLRLQMTDGH ISCTAVEFSY MSKISLNTPP GTKVKLSGIV DIKNGFLLLN DSNTTVLGGE 

        70         80         90        100        110        120 
VEHLIEKWEL QRSLSKHNRS NIGTEGGPPP FVPFGQKCVS HVQVDSRELD RRKTLQVTMP 

       130        140        150        160        170        180 
VKPTNDNDEF EKQRTAAIAE VAKSKETKTF GGGGGGARSN LNMNAAGNRN REVLQKEKST 

       190        200        210        220        230        240 
KSEGKHEGVY RELVDEKALK HITEMGFSKE ASRQALMDNG NNLEAALNVL LTSNKQKPVM 

       250        260        270        280        290        300 
GPPLRGRGKG RGRIRSEDEE DLGNARPSAP STLFDFLESK MGTLNVEEPK SQPQQLHQGQ 

       310        320        330        340        350        360 
YRSSNTEQNG VKDNNHLRHP PRNDTRQPRN EKPPRFQRDS QNSKSVLEGS GLPRNRGSER 

       370        380        390        400        410        420 
PSTSSVSEVW AEDRIKCDRP YSRYDRTKDT SYPLGSQHSD GAFKKRDNSM QSRSGKGPSF 

       430        440        450        460        470        480 
AEAKENPLPQ GSVDYNNQKR GKRESQTSIP DYFYDRKSQT INNEAFSGIK IEKHFNVNTD 

       490        500        510        520        530        540 
YQNPVRSNSF IGVPNGEVEM PLKGRRIGPI KPAGPVTAVP CDDKIFYNSG PKRRSGPIKP 

       550        560        570        580        590        600 
EKILESSIPM EYAKMWKPGD ECFALYWEDN KFYRAEVEAL HSSGMTAVVK FIDYGNYEEV 

       610        620        630        640        650 
LLSNIKPIQT EAWEEEGTYD QTLEFRRGGD GQPRRSTRPT QQFYQPPRAR N 

« Hide

Isoform 2 (Long) [UniParc].

Checksum: 997FB4382F678469
Show »

FASTA65073,057
Isoform 3 [UniParc].

Checksum: CF27720025EFBD81
Show »

FASTA74483,103

References

« Hide 'large scale' references
[1]"TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules."
Goulet I., Boisvenue S., Mokas S., Mazroui R., Cote J.
Hum. Mol. Genet. 17:3055-3074(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), ALTERNATIVE SPLICING, FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF GLU-598, INTERACTION WITH EWSR1; FMR1; FUS; SERBP1; EEF1A1 AND DDX3X OR DDX3Y.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[3]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Fetal kidney.
[4]"The DNA sequence and analysis of human chromosome 13."
Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L., Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S., Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P., Ambrose K.D., Andrews D.T. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P., Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C., Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P., Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L., Frankish A.G., Frankland J., French L., Garner P., Garnett J., Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M., Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D., Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D., Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S., Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S., Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R., Rogers J., Ross M.T.
Nature 428:522-528(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: Placenta and Testis.
[7]"Tudor domains bind symmetrical dimethylated arginines."
Cote J., Richard S.
J. Biol. Chem. 280:28476-28483(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH SNRPB AND SNRPN.
[8]"Tdrd3 is a novel stress granule-associated protein interacting with the Fragile-X syndrome protein FMRP."
Linder B., Ploettner O., Kroiss M., Hartmann E., Laggerbauer B., Meister G., Keidel E., Fischer U.
Hum. Mol. Genet. 17:3236-3246(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LYS-48-LINKED TETRA-UBIQUITIN; FMR1; FXR1 AND FXR2, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[9]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-256, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-256, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[11]"SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay."
Kashima I., Jonas S., Jayachandran U., Buchwald G., Conti E., Lupas A.N., Izaurralde E.
Genes Dev. 24:2440-2450(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH THE EXON JUNCTION COMPLEX, MUTAGENESIS OF 638-ARG--TYR-644.
[12]"TDRD3 is an effector molecule for arginine-methylated histone marks."
Yang Y., Lu Y., Espejo A., Wu J., Xu W., Liang S., Bedford M.T.
Mol. Cell 40:1016-1023(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, DOMAIN TUDOR.
[13]"Solution structure of the UBA domain of human Tudor domain containing protein 3."
RIKEN structural genomics initiative (RSGI)
Submitted (NOV-2004) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 194-243.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS53872.1. [Q9H7E2-3]
CCDS9441.1. [Q9H7E2-1]
RefSeqNP_001139542.1. NM_001146070.1. [Q9H7E2-3]
NP_001139543.1. NM_001146071.1. [Q9H7E2-1]
NP_110421.1. NM_030794.2. [Q9H7E2-1]
XP_005266615.1. XM_005266558.2. [Q9H7E2-3]
UniGeneHs.525061.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalQ9H7E2.
SMRQ9H7E2. Positions 1-68, 194-243, 548-608.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid123514. 12 interactions.
IntActQ9H7E2. 1 interaction.
STRING9606.ENSP00000196169.

PTM databases

PhosphoSiteQ9H7E2.

Polymorphism databases

DMDM29337133.

Proteomic databases

MaxQBQ9H7E2.
PaxDbQ9H7E2.
PRIDEQ9H7E2.

Protocols and materials databases

DNASU81550.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000196169; ENSP00000196169; ENSG00000083544. [Q9H7E2-1]
ENST00000377881; ENSP00000367113; ENSG00000083544. [Q9H7E2-1]
ENST00000377894; ENSP00000367126; ENSG00000083544. [Q9H7E2-1]
ENST00000535286; ENSP00000440190; ENSG00000083544. [Q9H7E2-3]
GeneID81550.
KEGGhsa:81550.
UCSCuc001vhz.4. human. [Q9H7E2-1]
uc001vib.4. human. [Q9H7E2-2]
uc010aeg.3. human. [Q9H7E2-3]

Organism-specific databases

CTD81550.
GeneCardsGC13P060970.
HGNCHGNC:20612. TDRD3.
HPACAB034925.
MIM614392. gene.
neXtProtNX_Q9H7E2.
PharmGKBPA134962690.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG300229.
HOGENOMHOG000154539.
HOVERGENHBG059153.
InParanoidQ9H7E2.
OMACVLQIQK.
OrthoDBEOG7F7W8R.
PhylomeDBQ9H7E2.
TreeFamTF316491.

Gene expression databases

ArrayExpressQ9H7E2.
BgeeQ9H7E2.
CleanExHS_TDRD3.
GenevestigatorQ9H7E2.

Family and domain databases

InterProIPR002999. Tudor.
IPR009060. UBA-like.
IPR015940. UBA/transl_elong_EF1B_N_euk.
IPR000449. UBA/Ts_N.
[Graphical view]
PfamPF00567. TUDOR. 1 hit.
PF00627. UBA. 1 hit.
[Graphical view]
SMARTSM00333. TUDOR. 1 hit.
SM00165. UBA. 1 hit.
[Graphical view]
SUPFAMSSF46934. SSF46934. 1 hit.
PROSITEPS50304. TUDOR. 1 hit.
PS50030. UBA. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSTDRD3. human.
EvolutionaryTraceQ9H7E2.
GeneWikiTDRD3.
GenomeRNAi81550.
NextBio71791.
PROQ9H7E2.
SOURCESearch...

Entry information

Entry nameTDRD3_HUMAN
AccessionPrimary (citable) accession number: Q9H7E2
Secondary accession number(s): B2MWP9, Q53XA6, Q6P992
Entry history
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: March 1, 2001
Last modified: July 9, 2014
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 13

Human chromosome 13: entries, gene names and cross-references to MIM