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Q96F86 (EDC3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 112. 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·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Enhancer of mRNA-decapping protein 3
Alternative name(s):
LSM16 homolog
YjeF N-terminal domain-containing protein 2
Short name=YjeF_N2
Short name=hYjeF_N2
YjeF domain-containing protein 1
Gene names
Name:EDC3
Synonyms:LSM16, YJDC, YJEFN2
ORF Names:PP844
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length508 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Binds single-stranded RNA. In the process of mRNA degradation, may play a role in mRNA decapping. May play a role in spermiogenesis and oogenesis. Ref.5 Ref.7 Ref.15

Subunit structure

Homodimer (via YjeF N-terminal domain). Forms a complex with DCP1A, DCP2, DDX6 and EDC4/HEDLS, within this complex directly interacts with DCP1A and DDX6. Interacts with ZFP36. Ref.5 Ref.15 Ref.16

Subcellular location

CytoplasmP-body. Note: Processing bodies (PB). Ref.5

Tissue specificity

Expressed in theca and granulosa cells in ovary, and in spermatids of the meiotic division part II and apical membrane of Sertoli cells in testis (at protein level). Also expressed in brain and mammary gland. Ref.7

Domain

The DFDF domain is unstructured by itself. It assumes a helical fold upon interaction with DDX6. Ref.16

Sequence similarities

Belongs to the EDC3 family.

Contains 1 DFDF domain.

Contains 1 YjeF N-terminal domain.

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 508508Enhancer of mRNA-decapping protein 3
PRO_0000119054

Regions

Domain192 – 22837DFDF
Domain283 – 487205YjeF N-terminal
Region1 – 7979Required for P-body targeting and interaction with DCP1A By similarity
Region191 – 296106Required for interaction with DDX6 By similarity

Amino acid modifications

Modified residue1311Phosphoserine Ref.6 Ref.8
Modified residue1381Phosphoserine Ref.13
Modified residue1401Phosphoserine Ref.13
Modified residue1611Phosphoserine Ref.10 Ref.11

Experimental info

Mutagenesis2041F → A: Abolishes interaction with DDX6; when associated with A-206. Ref.16
Mutagenesis2061F → A: Abolishes interaction with DDX6; when associated with A-204. Ref.16
Mutagenesis3061E → A: Abolishes homodimerization and RNA binding; when associated with A-310. Ref.15
Mutagenesis3101V → A: Abolishes homodimerization and RNA binding; when associated with A-306. Ref.15
Sequence conflict741Q → R in BAB15001. Ref.2

Secondary structure

............................................................ 508
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q96F86 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: 95346F484FCFC3EA

FASTA50856,078
        10         20         30         40         50         60 
MATDWLGSIV SINCGDSLGV YQGRVSAVDQ VSQTISLTRP FHNGVKCLVP EVTFRAGDIT 

        70         80         90        100        110        120 
ELKILEIPGP GDNQHFGDLH QTELGPSGAG CQVGINQNGT GKFVKKPASS SSAPQNIPKR 

       130        140        150        160        170        180 
TDVKSQDVAV SPQQQQCSKS YVDRHMESLS QSKSFRRRHN SWSSSSRHPN QATPKKSGLK 

       190        200        210        220        230        240 
NGQMKNKDDE CFGDDIEEIP DTDFDFEGNL ALFDKAAVFE EIDTYERRSG TRSRGIPNER 

       250        260        270        280        290        300 
PTRYRHDENI LESEPIVYRR IIVPHNVSKE FCTDSGLVVP SISYELHKKL LSVAEKHGLT 

       310        320        330        340        350        360 
LERRLEMTGV CASQMALTLL GGPNRLNPKN VHQRPTVALL CGPHVKGAQG ISCGRHLANH 

       370        380        390        400        410        420 
DVQVILFLPN FVKMLESITN ELSLFSKTQG QQVSSLKDLP TSPVDLVINC LDCPENVFLR 

       430        440        450        460        470        480 
DQPWYKAAVA WANQNRAPVL SIDPPVHEVE QGIDAKWSLA LGLPLPLGEH AGRIYLCDIG 

       490        500 
IPQQVFQEVG INYHSPFGCK FVIPLHSA 

« Hide

References

« Hide 'large scale' references
[1]"Large-scale cDNA transfection screening for genes related to cancer development and progression."
Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X. expand/collapse author list , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J.
Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[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].
[3]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 (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"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].
Tissue: Eye and Placenta.
[5]"Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping."
Fenger-Groen M., Fillman C., Norrild B., Lykke-Andersen J.
Mol. Cell 20:905-915(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH DCP1A; DCP2; DDX6; EDC4 AND ZFP36, SUBCELLULAR LOCATION, FUNCTION.
[6]"A probability-based approach for high-throughput protein phosphorylation analysis and site localization."
Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.
Nat. Biotechnol. 24:1285-1292(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[7]"ApoA-I-binding protein (AI-BP) and its homologues hYjeF_N2 and hYjeF_N3 comprise the YjeF_N domain protein family in humans with a role in spermiogenesis and oogenesis."
Rudolph C., Sigruener A., Hartmann A., Orso E., Bals-Pratsch M., Gronwald W., Seifert B., Kalbitzer H.R., Verdorfer I., Luetjens C.M., Ortmann O., Bornstein S.R., Schmitz G.
Horm. Metab. Res. 39:322-335(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, TISSUE SPECIFICITY.
[8]"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-131, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[9]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[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-161, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[11]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-161, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[12]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138 AND SER-140, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting."
Tritschler F., Eulalio A., Truffault V., Hartmann M.D., Helms S., Schmidt S., Coles M., Izaurralde E., Weichenrieder O.
Mol. Cell. Biol. 27:8600-8611(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.31 ANGSTROMS) OF 1-82.
[15]"Crystal structure of human Edc3 and its functional implications."
Ling S.H., Decker C.J., Walsh M.A., She M., Parker R., Song H.
Mol. Cell. Biol. 28:5965-5976(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 250-508, FUNCTION, RNA-BINDING, SUBUNIT, CIRCULAR DICHROISM, MUTAGENESIS OF GLU-306 AND VAL-310.
[16]"Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B."
Tritschler F., Braun J.E., Eulalio A., Truffault V., Izaurralde E., Weichenrieder O.
Mol. Cell 33:661-668(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 192-228 IN COMPLEX WITH DDX6, INTERACTION WITH DDX6, MUTAGENESIS OF PHE-204 AND PHE-206, DOMAIN.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF193058 mRNA. Translation: AAG22486.1.
AK024781 mRNA. Translation: BAB15001.1.
AK056339 mRNA. Translation: BAG51682.1.
CH471136 Genomic DNA. Translation: EAW99316.1.
CH471136 Genomic DNA. Translation: EAW99317.1.
CH471136 Genomic DNA. Translation: EAW99318.1.
CH471136 Genomic DNA. Translation: EAW99319.1.
BC011534 mRNA. Translation: AAH11534.1.
BC021271 mRNA. Translation: AAH21271.1.
CCDSCCDS10267.1.
RefSeqNP_001135915.1. NM_001142443.1.
NP_001135916.1. NM_001142444.1.
NP_079359.2. NM_025083.3.
UniGeneHs.682454.
Hs.96852.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2VC8X-ray1.31A1-82[»]
2WAXX-ray2.30B/D192-228[»]
2WAYX-ray2.30B/D192-228[»]
3D3JX-ray2.80A203-508[»]
3D3KX-ray2.20A/B/C/D250-508[»]
ProteinModelPortalQ96F86.
SMRQ96F86. Positions 3-74, 197-226, 258-507.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid123144. 15 interactions.
DIPDIP-35516N.
IntActQ96F86. 14 interactions.
MINTMINT-5005528.
STRING9606.ENSP00000320503.

PTM databases

PhosphoSiteQ96F86.

Polymorphism databases

DMDM74731669.

Proteomic databases

MaxQBQ96F86.
PaxDbQ96F86.
PeptideAtlasQ96F86.
PRIDEQ96F86.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000315127; ENSP00000320503; ENSG00000179151.
ENST00000426797; ENSP00000401343; ENSG00000179151.
ENST00000568176; ENSP00000455580; ENSG00000179151.
GeneID80153.
KEGGhsa:80153.
UCSCuc002aym.3. human.

Organism-specific databases

CTD80153.
GeneCardsGC15M074922.
HGNCHGNC:26114. EDC3.
HPAHPA040650.
HPA044206.
MIM609842. gene.
neXtProtNX_Q96F86.
PharmGKBPA142670551.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG271303.
HOGENOMHOG000231481.
HOVERGENHBG079428.
InParanoidQ96F86.
KOK12615.
OMAPEVTFRA.
OrthoDBEOG7H793B.
PhylomeDBQ96F86.
TreeFamTF324695.

Enzyme and pathway databases

ReactomeREACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpressQ96F86.
BgeeQ96F86.
CleanExHS_EDC3.
GenevestigatorQ96F86.

Family and domain databases

Gene3D3.40.50.10260. 1 hit.
InterProIPR025762. DFDF.
IPR019050. FDF_dom.
IPR025609. Lsm14_N.
IPR004443. YjeF_N_dom.
[Graphical view]
PfamPF09532. FDF. 1 hit.
PF12701. LSM14. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]
SUPFAMSSF64153. SSF64153. 1 hit.
PROSITEPS51512. DFDF. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ96F86.
GeneWikiEDC3.
GenomeRNAi80153.
NextBio70444.
PROQ96F86.
SOURCESearch...

Entry information

Entry nameEDC3_HUMAN
AccessionPrimary (citable) accession number: Q96F86
Secondary accession number(s): B3KPH0, D3DW61, Q9H797
Entry history
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: December 1, 2001
Last modified: July 9, 2014
This is version 112 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 15

Human chromosome 15: entries, gene names and cross-references to MIM