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Protein

116 kDa U5 small nuclear ribonucleoprotein component

Gene

EFTUD2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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
  • RNA binding Source: UniProtKB

GO - Biological processi

  • cellular response to drug Source: Ensembl
  • mRNA processing Source: ProtInc
  • mRNA splicing, via spliceosome Source: GO_Central
  • response to cocaine Source: Ensembl
  • RNA splicing Source: ProtInc

Keywordsi

Biological processmRNA processing, mRNA splicing
LigandGTP-binding, Nucleotide-binding

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000108883.12
HGNCiHGNC:30858 EFTUD2
MIMi603892 gene
neXtProtiNX_Q15029

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

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 dbSNP:rs387906877EnsemblClinVar.1
Natural variantiVAR_067581476C → R in MFDM. 1 Publication1
Natural variantiVAR_067582637L → R in MFDM. 1 PublicationCorresponds to variant dbSNP:rs387906879EnsemblClinVar.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); alternateCombined sources
Cross-linki64Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei86PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ15029
MaxQBiQ15029
PaxDbiQ15029
PeptideAtlasiQ15029
PRIDEiQ15029
ProteomicsDBi60379

PTM databases

iPTMnetiQ15029
PhosphoSitePlusiQ15029
SwissPalmiQ15029

Expressioni

Gene expression databases

BgeeiENSG00000108883 Expressed in 196 organ(s), highest expression level in skeletal muscle tissue
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

Protein-protein interaction databases

BioGridi114749, 183 interactors
CORUMiQ15029
IntActiQ15029, 58 interactors
MINTiQ15029
STRINGi9606.ENSP00000392094

Structurei

3D structure databases

ProteinModelPortaliQ15029
SMRiQ15029
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG0469 Eukaryota
COG0480 LUCA
GeneTreeiENSGT00930000150948
HOGENOMiHOG000231589
HOVERGENiHBG001838
InParanoidiQ15029
KOiK12852
OMAiGPDEMGP
OrthoDBiEOG091G017G
PhylomeDBiQ15029
TreeFamiTF105703

Family and domain databases

CDDicd04098 eEF2_C_snRNP, 1 hit
Gene3Di3.30.230.10, 1 hit
InterProiView protein in InterPro
IPR035647 EFG_III/V
IPR000640 EFG_V-like
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_sf
IPR005517 Transl_elong_EFG/EF2_IV
IPR035655 U5-116kDa_C
PfamiView protein in Pfam
PF00679 EFG_C, 1 hit
PF03764 EFG_IV, 1 hit
PF16004 EFTUD2, 1 hit
PF00009 GTP_EFTU, 1 hit
PF03144 GTP_EFTU_D2, 1 hit
PRINTSiPR00315 ELONGATNFCT
SMARTiView protein in SMART
SM00838 EFG_C, 1 hit
SM00889 EFG_IV, 1 hit
SUPFAMiSSF50447 SSF50447, 1 hit
SSF52540 SSF52540, 1 hit
SSF54211 SSF54211, 1 hit
SSF54980 SSF54980, 2 hits
TIGRFAMsiTIGR00231 small_GTP, 1 hit
PROSITEiView protein in PROSITE
PS51722 G_TR_2, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

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

This entry has 3 described isoforms and 6 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
K7EP67K7EP67_HUMAN
116 kDa U5 small nuclear ribonucleo...
EFTUD2
223Annotation score:
K7EJ74K7EJ74_HUMAN
116 kDa U5 small nuclear ribonucleo...
EFTUD2
134Annotation score:
K7EIT3K7EIT3_HUMAN
116 kDa U5 small nuclear ribonucleo...
EFTUD2
148Annotation score:
K7EIV5K7EIV5_HUMAN
116 kDa U5 small nuclear ribonucleo...
EFTUD2
106Annotation score:
K7EQ26K7EQ26_HUMAN
116 kDa U5 small nuclear ribonucleo...
EFTUD2
33Annotation score:
K7ERJ5K7ERJ5_HUMAN
116 kDa U5 small nuclear ribonucleo...
EFTUD2
38Annotation score:

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 dbSNP:rs387906877EnsemblClinVar.1
Natural variantiVAR_067581476C → R in MFDM. 1 Publication1
Natural variantiVAR_067582637L → R in MFDM. 1 PublicationCorresponds to variant dbSNP:rs387906879EnsemblClinVar.1
Natural variantiVAR_014931773G → V. Corresponds to variant dbSNP:rs1056505Ensembl.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

Similar proteinsi

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[»]
5MQFelectron microscopy5.90B1-972[»]
5O9Zelectron microscopy4.50B1-972[»]
5XJCelectron microscopy3.60C1-972[»]
5YZGelectron microscopy4.10C1-972[»]
5Z56electron microscopy5.10C1-972[»]
5Z57electron microscopy6.50C1-972[»]
5Z58electron microscopy4.90C1-972[»]
6FF4electron microscopy16.00B1-972[»]
ProteinModelPortaliQ15029
SMRiQ15029
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114749, 183 interactors
CORUMiQ15029
IntActiQ15029, 58 interactors
MINTiQ15029
STRINGi9606.ENSP00000392094

PTM databases

iPTMnetiQ15029
PhosphoSitePlusiQ15029
SwissPalmiQ15029

Polymorphism and mutation databases

BioMutaiEFTUD2
DMDMi18202501

Proteomic databases

EPDiQ15029
MaxQBiQ15029
PaxDbiQ15029
PeptideAtlasiQ15029
PRIDEiQ15029
ProteomicsDBi60379

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
EuPathDBiHostDB:ENSG00000108883.12
GeneCardsiEFTUD2
H-InvDBiHIX0135614
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
GeneTreeiENSGT00930000150948
HOGENOMiHOG000231589
HOVERGENiHBG001838
InParanoidiQ15029
KOiK12852
OMAiGPDEMGP
OrthoDBiEOG091G017G
PhylomeDBiQ15029
TreeFamiTF105703

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway

Miscellaneous databases

ChiTaRSiEFTUD2 human
GeneWikiiEFTUD2
GenomeRNAii9343
PROiPR:Q15029
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000108883 Expressed in 196 organ(s), highest expression level in skeletal muscle tissue
CleanExiHS_EFTUD2
ExpressionAtlasiQ15029 baseline and differential
GenevisibleiQ15029 HS

Family and domain databases

CDDicd04098 eEF2_C_snRNP, 1 hit
Gene3Di3.30.230.10, 1 hit
InterProiView protein in InterPro
IPR035647 EFG_III/V
IPR000640 EFG_V-like
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_sf
IPR005517 Transl_elong_EFG/EF2_IV
IPR035655 U5-116kDa_C
PfamiView protein in Pfam
PF00679 EFG_C, 1 hit
PF03764 EFG_IV, 1 hit
PF16004 EFTUD2, 1 hit
PF00009 GTP_EFTU, 1 hit
PF03144 GTP_EFTU_D2, 1 hit
PRINTSiPR00315 ELONGATNFCT
SMARTiView protein in SMART
SM00838 EFG_C, 1 hit
SM00889 EFG_IV, 1 hit
SUPFAMiSSF50447 SSF50447, 1 hit
SSF52540 SSF52540, 1 hit
SSF54211 SSF54211, 1 hit
SSF54980 SSF54980, 2 hits
TIGRFAMsiTIGR00231 small_GTP, 1 hit
PROSITEiView protein in PROSITE
PS51722 G_TR_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiU5S1_HUMAN
AccessioniPrimary (citable) accession number: Q15029
Secondary accession number(s): B4DK30
, B4DMC0, D3DX58, K7EJ81, Q9BUR0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: November 1, 1996
Last modified: November 7, 2018
This is version 210 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. SIMILARITY comments
    Index of protein domains and families
  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. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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