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Protein

116 kDa U5 small nuclear ribonucleoprotein component

Gene

EFTUD2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the U5 snRNP and the U4/U6-U5 tri-snRNP complex required for pre-mRNA splicing. Binds GTP.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi136 – 143GTPSequence analysis8
Nucleotide bindingi204 – 208GTPSequence analysis5
Nucleotide bindingi258 – 261GTPSequence analysis4

GO - Molecular functioni

  • GTPase activity Source: ProtInc
  • GTP binding Source: UniProtKB-KW
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • cellular response to drug Source: Ensembl
  • mRNA processing Source: ProtInc
  • mRNA splicing, via spliceosome Source: UniProtKB
  • response to cocaine Source: Ensembl
  • RNA splicing Source: ProtInc
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000108883-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
116 kDa U5 small nuclear ribonucleoprotein component
Alternative name(s):
Elongation factor Tu GTP-binding domain-containing protein 2
SNU114 homolog
Short name:
hSNU114
U5 snRNP-specific protein, 116 kDa
Short name:
U5-116 kDa
Gene namesi
Name:EFTUD2
Synonyms:KIAA0031, SNRP116
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:30858. EFTUD2.

Subcellular locationi

GO - Cellular componenti

  • Cajal body Source: BHF-UCL
  • catalytic step 2 spliceosome Source: UniProtKB
  • cytoplasm Source: HPA
  • extracellular matrix Source: BHF-UCL
  • membrane Source: UniProtKB
  • nuclear speck Source: BHF-UCL
  • nucleoplasm Source: HPA
  • spliceosomal complex Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Involvement in diseasei

Mandibulofacial dysostosis with microcephaly (MFDM)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA rare syndrome characterized by progressive microcephaly, midface and malar hypoplasia, micrognathia, microtia, dysplastic ears, preauricular skin tags, significant developmental delay, and speech delay. Many patients have major sequelae, including choanal atresia that results in respiratory difficulties, conductive hearing loss, and cleft palate.
See also OMIM:610536
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_067580262R → W in MFDM. 1 PublicationCorresponds to variant rs387906877dbSNPEnsembl.1
Natural variantiVAR_067581476C → R in MFDM. 1 Publication1
Natural variantiVAR_067582637L → R in MFDM. 1 PublicationCorresponds to variant rs387906879dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi9343.
MalaCardsiEFTUD2.
MIMi610536. phenotype.
OpenTargetsiENSG00000108883.
Orphaneti79113. Mandibulofacial dysostosis-microcephaly syndrome.
PharmGKBiPA142671915.

Polymorphism and mutation databases

BioMutaiEFTUD2.
DMDMi18202501.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000915631 – 972116 kDa U5 small nuclear ribonucleoprotein componentAdd BLAST972

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei19PhosphoserineCombined sources1
Cross-linki64Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)Combined sources
Modified residuei86PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ15029.
MaxQBiQ15029.
PaxDbiQ15029.
PeptideAtlasiQ15029.
PRIDEiQ15029.

PTM databases

iPTMnetiQ15029.
PhosphoSitePlusiQ15029.
SwissPalmiQ15029.

Expressioni

Gene expression databases

BgeeiENSG00000108883.
CleanExiHS_EFTUD2.
ExpressionAtlasiQ15029. baseline and differential.
GenevisibleiQ15029. HS.

Organism-specific databases

HPAiHPA022021.

Interactioni

Subunit structurei

Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39. Identified in the spliceosome C complex. Interacts with ERBB4 and PRPF8. Interacts with PIH1D1 (PubMed:24656813).5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
HSPB1P047922EBI-357897,EBI-352682
IKQ131232EBI-357897,EBI-713456
MYCP011065EBI-357897,EBI-447544
PRPF8Q6P2Q92EBI-357897,EBI-538479
SF3B4Q154272EBI-357897,EBI-348469

Protein-protein interaction databases

BioGridi114749. 150 interactors.
IntActiQ15029. 54 interactors.
MINTiMINT-1161890.
STRINGi9606.ENSP00000392094.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.00B1-972[»]
ProteinModelPortaliQ15029.
SMRiQ15029.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini127 – 409tr-type GPROSITE-ProRule annotationAdd BLAST283

Sequence similaritiesi

Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily.PROSITE-ProRule annotation
Contains 1 tr-type G (guanine nucleotide-binding) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0469. Eukaryota.
COG0480. LUCA.
GeneTreeiENSGT00860000133864.
HOGENOMiHOG000231589.
HOVERGENiHBG001838.
InParanoidiQ15029.
KOiK12852.
OMAiPTDTSIK.
OrthoDBiEOG091G017G.
PhylomeDBiQ15029.
TreeFamiTF105703.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.70.240. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR009022. EFG_III-V.
IPR000640. EFG_V.
IPR004161. EFTu-like_2.
IPR031950. EFTUD2_N.
IPR027417. P-loop_NTPase.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR005225. Small_GTP-bd_dom.
IPR000795. TF_GTP-bd_dom.
IPR009000. Transl_B-barrel.
IPR005517. Transl_elong_EFG/EF2_IV.
[Graphical view]
PfamiPF00679. EFG_C. 1 hit.
PF14492. EFG_II. 1 hit.
PF03764. EFG_IV. 1 hit.
PF16004. EFTUD2. 1 hit.
PF03144. GTP_EFTU_D2. 1 hit.
[Graphical view]
PRINTSiPR00315. ELONGATNFCT.
SMARTiSM00838. EFG_C. 1 hit.
SM00889. EFG_IV. 1 hit.
[Graphical view]
SUPFAMiSSF50447. SSF50447. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF54211. SSF54211. 1 hit.
SSF54980. SSF54980. 2 hits.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51722. G_TR_2. 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: Q15029-1) [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
MDTDLYDEFG NYIGPELDSD EDDDELGRET KDLDEMDDDD DDDDVGDHDD
60 70 80 90 100
DHPGMEVVLH EDKKYYPTAE EVYGPEVETI VQEEDTQPLT EPIIKPVKTK
110 120 130 140 150
KFTLMEQTLP VTVYEMDFLA DLMDNSELIR NVTLCGHLHH GKTCFVDCLI
160 170 180 190 200
EQTHPEIRKR YDQDLCYTDI LFTEQERGVG IKSTPVTVVL PDTKGKSYLF
210 220 230 240 250
NIMDTPGHVN FSDEVTAGLR ISDGVVLFID AAEGVMLNTE RLIKHAVQER
260 270 280 290 300
LAVTVCINKI DRLILELKLP PTDAYYKLRH IVDEVNGLIS MYSTDENLIL
310 320 330 340 350
SPLLGNVCFS SSQYSICFTL GSFAKIYADT FGDINYQEFA KRLWGDIYFN
360 370 380 390 400
PKTRKFTKKA PTSSSQRSFV EFILEPLYKI LAQVVGDVDT SLPRTLDELG
410 420 430 440 450
IHLTKEELKL NIRPLLRLVC KKFFGEFTGF VDMCVQHIPS PKVGAKPKIE
460 470 480 490 500
HTYTGGVDSD LGEAMSDCDP DGPLMCHTTK MYSTDDGVQF HAFGRVLSGT
510 520 530 540 550
IHAGQPVKVL GENYTLEDEE DSQICTVGRL WISVARYHIE VNRVPAGNWV
560 570 580 590 600
LIEGVDQPIV KTATITEPRG NEEAQIFRPL KFNTTSVIKI AVEPVNPSEL
610 620 630 640 650
PKMLDGLRKV NKSYPSLTTK VEESGEHVIL GTGELYLDCV MHDLRKMYSE
660 670 680 690 700
IDIKVADPVV TFCETVVETS SLKCFAETPN KKNKITMIAE PLEKGLAEDI
710 720 730 740 750
ENEVVQITWN RKKLGEFFQT KYDWDLLAAR SIWAFGPDAT GPNILVDDTL
760 770 780 790 800
PSEVDKALLG SVKDSIVQGF QWGTREGPLC DELIRNVKFK ILDAVVAQEP
810 820 830 840 850
LHRGGGQIIP TARRVVYSAF LMATPRLMEP YYFVEVQAPA DCVSAVYTVL
860 870 880 890 900
ARRRGHVTQD APIPGSPLYT IKAFIPAIDS FGFETDLRTH TQGQAFSLSV
910 920 930 940 950
FHHWQIVPGD PLDKSIVIRP LEPQPAPHLA REFMIKTRRR KGLSEDVSIS
960 970
KFFDDPMLLE LAKQDVVLNY PM
Length:972
Mass (Da):109,436
Last modified:November 1, 1996 - v1
Checksum:i862BD6CA7993F118
GO
Isoform 2 (identifier: Q15029-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-35: Missing.

Show »
Length:937
Mass (Da):105,384
Checksum:iC754AB346695B0C3
GO
Isoform 3 (identifier: Q15029-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     143-152: Missing.

Note: No experimental confirmation available.
Show »
Length:962
Mass (Da):108,283
Checksum:i6EF1ECDE3BDA0784
GO

Sequence cautioni

The sequence BAA04699 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti321G → V in AAH02360 (PubMed:15489334).Curated1
Sequence conflicti619T → S in BAG59832 (PubMed:14702039).Curated1
Sequence conflicti955D → G in BAG59832 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_067580262R → W in MFDM. 1 PublicationCorresponds to variant rs387906877dbSNPEnsembl.1
Natural variantiVAR_067581476C → R in MFDM. 1 Publication1
Natural variantiVAR_067582637L → R in MFDM. 1 PublicationCorresponds to variant rs387906879dbSNPEnsembl.1
Natural variantiVAR_014931773G → V.Corresponds to variant rs1056505dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0442821 – 35Missing in isoform 2. 1 PublicationAdd BLAST35
Alternative sequenceiVSP_055175143 – 152Missing in isoform 3. 1 Publication10

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D21163 mRNA. Translation: BAA04699.2. Different initiation.
AK296367 mRNA. Translation: BAG59042.1.
AK297392 mRNA. Translation: BAG59832.1.
AK316098 mRNA. Translation: BAH14469.1.
AC015936 Genomic DNA. No translation available.
CH471178 Genomic DNA. Translation: EAW51573.1.
CH471178 Genomic DNA. Translation: EAW51574.1.
BC002360 mRNA. Translation: AAH02360.1.
CCDSiCCDS11489.1. [Q15029-1]
CCDS45707.1. [Q15029-2]
CCDS59295.1. [Q15029-3]
RefSeqiNP_001136077.1. NM_001142605.1. [Q15029-2]
NP_001245282.1. NM_001258353.1. [Q15029-1]
NP_001245283.1. NM_001258354.1. [Q15029-3]
NP_004238.3. NM_004247.3. [Q15029-1]
UniGeneiHs.151787.

Genome annotation databases

EnsembliENST00000402521; ENSP00000385873; ENSG00000108883. [Q15029-2]
ENST00000426333; ENSP00000392094; ENSG00000108883. [Q15029-1]
ENST00000591382; ENSP00000467805; ENSG00000108883. [Q15029-1]
ENST00000592576; ENSP00000465058; ENSG00000108883. [Q15029-3]
GeneIDi9343.
KEGGihsa:9343.
UCSCiuc002ihn.3. human. [Q15029-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D21163 mRNA. Translation: BAA04699.2. Different initiation.
AK296367 mRNA. Translation: BAG59042.1.
AK297392 mRNA. Translation: BAG59832.1.
AK316098 mRNA. Translation: BAH14469.1.
AC015936 Genomic DNA. No translation available.
CH471178 Genomic DNA. Translation: EAW51573.1.
CH471178 Genomic DNA. Translation: EAW51574.1.
BC002360 mRNA. Translation: AAH02360.1.
CCDSiCCDS11489.1. [Q15029-1]
CCDS45707.1. [Q15029-2]
CCDS59295.1. [Q15029-3]
RefSeqiNP_001136077.1. NM_001142605.1. [Q15029-2]
NP_001245282.1. NM_001258353.1. [Q15029-1]
NP_001245283.1. NM_001258354.1. [Q15029-3]
NP_004238.3. NM_004247.3. [Q15029-1]
UniGeneiHs.151787.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.00B1-972[»]
ProteinModelPortaliQ15029.
SMRiQ15029.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114749. 150 interactors.
IntActiQ15029. 54 interactors.
MINTiMINT-1161890.
STRINGi9606.ENSP00000392094.

PTM databases

iPTMnetiQ15029.
PhosphoSitePlusiQ15029.
SwissPalmiQ15029.

Polymorphism and mutation databases

BioMutaiEFTUD2.
DMDMi18202501.

Proteomic databases

EPDiQ15029.
MaxQBiQ15029.
PaxDbiQ15029.
PeptideAtlasiQ15029.
PRIDEiQ15029.

Protocols and materials databases

DNASUi9343.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000402521; ENSP00000385873; ENSG00000108883. [Q15029-2]
ENST00000426333; ENSP00000392094; ENSG00000108883. [Q15029-1]
ENST00000591382; ENSP00000467805; ENSG00000108883. [Q15029-1]
ENST00000592576; ENSP00000465058; ENSG00000108883. [Q15029-3]
GeneIDi9343.
KEGGihsa:9343.
UCSCiuc002ihn.3. human. [Q15029-1]

Organism-specific databases

CTDi9343.
DisGeNETi9343.
GeneCardsiEFTUD2.
H-InvDBHIX0135614.
HGNCiHGNC:30858. EFTUD2.
HPAiHPA022021.
MalaCardsiEFTUD2.
MIMi603892. gene.
610536. phenotype.
neXtProtiNX_Q15029.
OpenTargetsiENSG00000108883.
Orphaneti79113. Mandibulofacial dysostosis-microcephaly syndrome.
PharmGKBiPA142671915.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0469. Eukaryota.
COG0480. LUCA.
GeneTreeiENSGT00860000133864.
HOGENOMiHOG000231589.
HOVERGENiHBG001838.
InParanoidiQ15029.
KOiK12852.
OMAiPTDTSIK.
OrthoDBiEOG091G017G.
PhylomeDBiQ15029.
TreeFamiTF105703.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000108883-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

ChiTaRSiEFTUD2. human.
GeneWikiiEFTUD2.
GenomeRNAii9343.
PROiQ15029.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000108883.
CleanExiHS_EFTUD2.
ExpressionAtlasiQ15029. baseline and differential.
GenevisibleiQ15029. HS.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.70.240. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR009022. EFG_III-V.
IPR000640. EFG_V.
IPR004161. EFTu-like_2.
IPR031950. EFTUD2_N.
IPR027417. P-loop_NTPase.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR005225. Small_GTP-bd_dom.
IPR000795. TF_GTP-bd_dom.
IPR009000. Transl_B-barrel.
IPR005517. Transl_elong_EFG/EF2_IV.
[Graphical view]
PfamiPF00679. EFG_C. 1 hit.
PF14492. EFG_II. 1 hit.
PF03764. EFG_IV. 1 hit.
PF16004. EFTUD2. 1 hit.
PF03144. GTP_EFTU_D2. 1 hit.
[Graphical view]
PRINTSiPR00315. ELONGATNFCT.
SMARTiSM00838. EFG_C. 1 hit.
SM00889. EFG_IV. 1 hit.
[Graphical view]
SUPFAMiSSF50447. SSF50447. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF54211. SSF54211. 1 hit.
SSF54980. SSF54980. 2 hits.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51722. G_TR_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiU5S1_HUMAN
AccessioniPrimary (citable) accession number: Q15029
Secondary accession number(s): B4DK30
, B4DMC0, D3DX58, K7EJ81, Q9BUR0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: November 1, 1996
Last modified: November 30, 2016
This is version 190 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 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.