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Protein

Regulator of nonsense transcripts 3B

Gene

UPF3B

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

Functioni

Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF2 stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA upstream of exon-exon junctions. In vitro, stimulates translation; the function is independent of association with UPF2 and components of the EJC core.5 Publications

GO - Molecular functioni

  • mRNA binding Source: UniProtKB
  • nucleocytoplasmic transporter activity Source: UniProtKB
  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA transport, Nonsense-mediated mRNA decay, Transport

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.
R-HSA-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
Regulator of nonsense transcripts 3B
Alternative name(s):
Nonsense mRNA reducing factor 3B
Up-frameshift suppressor 3 homolog B
Short name:
hUpf3B
Up-frameshift suppressor 3 homolog on chromosome X
Short name:
hUpf3p-X
Gene namesi
Name:UPF3B
Synonyms:RENT3B, UPF3X
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:20439. UPF3B.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytosol Source: Reactome
  • exon-exon junction complex Source: UniProtKB
  • microtubule organizing center Source: HPA
  • nucleolus Source: HPA
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Mental retardation, X-linked, syndromic, 14 (MRXS14)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXS14 patients manifest mental retardation associated with other variable signs such as autistic features, slender build, poor musculature, long, thin face, high-arched palate, high nasal bridge, and pectus deformities.
See also OMIM:300676
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_037666160Y → D in MRXS14. 1 PublicationCorresponds to variant rs122468182dbSNPEnsembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi52K → E: Abolishes interaction with UPF2. 1 Publication1
Mutagenesisi53 – 58VVIRRL → AVARRA: Abolishes interaction with UPF2. 1 Publication6
Mutagenesisi56R → E: Does not abolish interaction with UPF2. 1 Publication1
Mutagenesisi117 – 119YVF → DVD: Abolishes interaction with UPF2. 1 Publication3
Mutagenesisi430R → A: Reduces NMD. 1 Publication1
Mutagenesisi432R → A: Reduces NMD. 2 Publications1
Mutagenesisi434 – 447Missing : Abolishes NMD. 1 PublicationAdd BLAST14
Mutagenesisi434K → A: Reduces NMD. 1 Publication1
Mutagenesisi435D → A: Reduces NMD. 1 Publication1
Mutagenesisi436R → A: Impairs association with EJC. 2 Publications1
Mutagenesisi436R → A: Reduces NMD. 2 Publications1
Mutagenesisi441L → F: Reduces NMD. 1 Publication1
Mutagenesisi442Y → A: Impairs association with EJC. 1 Publication1
Mutagenesisi447R → E: Abolishes NMD; when associated with E-449 and E-451. 1 Publication1
Mutagenesisi449R → E: Abolishes NMD; when associated with E-447 and E-451. 1 Publication1
Mutagenesisi451R → E: Abolishes NMD; when associated with E-447 and E-449. 1 Publication1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi65109.
MalaCardsiUPF3B.
MIMi300676. phenotype.
OpenTargetsiENSG00000125351.
Orphaneti323. FG syndrome.
776. X-linked intellectual disability with marfanoid habitus.
777. X-linked non-syndromic intellectual disability.
PharmGKBiPA128394708.

Polymorphism and mutation databases

BioMutaiUPF3B.
DMDMi60390643.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002152971 – 483Regulator of nonsense transcripts 3BAdd BLAST483

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei169PhosphothreonineCombined sources1
Modified residuei198PhosphothreonineCombined sources1
Modified residuei310PhosphoserineCombined sources1
Modified residuei447Omega-N-methylarginineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiQ9BZI7.
MaxQBiQ9BZI7.
PaxDbiQ9BZI7.
PeptideAtlasiQ9BZI7.
PRIDEiQ9BZI7.

PTM databases

iPTMnetiQ9BZI7.
PhosphoSitePlusiQ9BZI7.

Expressioni

Tissue specificityi

Expressed in testis, uterus, prostate, heart, muscle, brain, spinal cord and placenta.1 Publication

Gene expression databases

BgeeiENSG00000125351.
CleanExiHS_UPF3B.
ExpressionAtlasiQ9BZI7. baseline and differential.
GenevisibleiQ9BZI7. HS.

Organism-specific databases

HPAiHPA001592.
HPA001800.
HPA001882.

Interactioni

Subunit structurei

Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC); the EJC core components EIF4A3 and the MAGOH-RBM8A dimer form a composite binding site for UPF3B which overlaps with the EJC binding site for WIBG. Interacts with EST1A, UPF2 and RBM8A.9 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
EIF4A3P389197EBI-372780,EBI-299104
RBM8AQ9Y5S99EBI-372780,EBI-447231
UPF1Q929008EBI-372780,EBI-373471
UPF2Q9HAU57EBI-372780,EBI-372073

Protein-protein interaction databases

BioGridi122396. 44 interactors.
DIPiDIP-31143N.
IntActiQ9BZI7. 23 interactors.
MINTiMINT-265168.
STRINGi9606.ENSP00000276201.

Structurei

Secondary structure

1483
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi52 – 58Combined sources7
Helixi64 – 71Combined sources8
Beta strandi77 – 85Combined sources9
Beta strandi95 – 104Combined sources10
Helixi105 – 114Combined sources10
Beta strandi118 – 120Combined sources3
Beta strandi126 – 128Combined sources3
Beta strandi130 – 133Combined sources4
Turni433 – 435Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UW4X-ray1.95A/C50-140[»]
2XB2X-ray3.40G/U424-483[»]
ProteinModelPortaliQ9BZI7.
SMRiQ9BZI7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9BZI7.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni30 – 255Necessary for interaction with UPF2Add BLAST226
Regioni52 – 57Binds to UPF26
Regioni94 – 483Sufficient for association with EJC coreAdd BLAST390
Regioni430 – 447Necessary for interaction with RBM8A and for activating NMDAdd BLAST18

Sequence similaritiesi

Belongs to the RENT3 family.Curated

Phylogenomic databases

eggNOGiKOG1295. Eukaryota.
ENOG41122XD. LUCA.
GeneTreeiENSGT00390000017146.
HOGENOMiHOG000230909.
HOVERGENiHBG059714.
InParanoidiQ9BZI7.
KOiK14328.
OMAiRCPEKER.
OrthoDBiEOG091G0JKF.
PhylomeDBiQ9BZI7.
TreeFamiTF316034.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR005120. Nonsense_mediated_decay_UPF3.
IPR012677. Nucleotide-bd_a/b_plait.
[Graphical view]
PfamiPF03467. Smg4_UPF3. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BZI7-1) [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
MKEEKEHRPK EKRVTLLTPA GATGSGGGTS GDSSKGEDKQ DRNKEKKEAL
60 70 80 90 100
SKVVIRRLPP TLTKEQLQEH LQPMPEHDYF EFFSNDTSLY PHMYARAYIN
110 120 130 140 150
FKNQEDIILF RDRFDGYVFL DNKGQEYPAI VEFAPFQKAA KKKTKKRDTK
160 170 180 190 200
VGTIDDDPEY RKFLESYATD NEKMTSTPET LLEEIEAKNR ELIAKKTTPL
210 220 230 240 250
LSFLKNKQRM REEKREERRR REIERKRQRE EERRKWKEEE KRKRKDIEKL
260 270 280 290 300
KKIDRIPERD KLKDEPKIKV HRFLLQAVNQ KNLLKKPEKG DEKELDKREK
310 320 330 340 350
AKKLDKENLS DERASGQSCT LPKRSDSELK DEKPKRPEDE SGRDYRERER
360 370 380 390 400
EYERDQERIL RERERLKRQE EERRRQKERY EKEKTFKRKE EEMKKEKDTL
410 420 430 440 450
RDKGKKAEST ESIGSSEKTE KKEEVVKRDR IRNKDRPAMQ LYQPGARSRN
460 470 480
RLCPPDDSTK SGDSAAERKQ ESGISHRKEG GEE
Length:483
Mass (Da):57,762
Last modified:June 1, 2001 - v1
Checksum:iF5A8A395783D1A69
GO
Isoform 2 (identifier: Q9BZI7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     270-282: Missing.

Show »
Length:470
Mass (Da):56,213
Checksum:iC012044D45D9957F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti358R → H in AAI21018 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_037666160Y → D in MRXS14. 1 PublicationCorresponds to variant rs122468182dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_012963270 – 282Missing in isoform 2. 2 PublicationsAdd BLAST13

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY013251 mRNA. Translation: AAG48511.1.
AF318576 mRNA. Translation: AAG60691.1.
CH471161 Genomic DNA. Translation: EAW89842.1.
CH471161 Genomic DNA. Translation: EAW89844.1.
CH471161 Genomic DNA. Translation: EAW89845.1.
CH471161 Genomic DNA. Translation: EAW89846.1.
BC121017 mRNA. Translation: AAI21018.1.
CCDSiCCDS14587.1. [Q9BZI7-2]
CCDS14588.1. [Q9BZI7-1]
RefSeqiNP_075386.1. NM_023010.3. [Q9BZI7-2]
NP_542199.1. NM_080632.2. [Q9BZI7-1]
UniGeneiHs.103832.

Genome annotation databases

EnsembliENST00000276201; ENSP00000276201; ENSG00000125351. [Q9BZI7-1]
ENST00000345865; ENSP00000245418; ENSG00000125351. [Q9BZI7-2]
GeneIDi65109.
KEGGihsa:65109.
UCSCiuc004erz.3. human. [Q9BZI7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY013251 mRNA. Translation: AAG48511.1.
AF318576 mRNA. Translation: AAG60691.1.
CH471161 Genomic DNA. Translation: EAW89842.1.
CH471161 Genomic DNA. Translation: EAW89844.1.
CH471161 Genomic DNA. Translation: EAW89845.1.
CH471161 Genomic DNA. Translation: EAW89846.1.
BC121017 mRNA. Translation: AAI21018.1.
CCDSiCCDS14587.1. [Q9BZI7-2]
CCDS14588.1. [Q9BZI7-1]
RefSeqiNP_075386.1. NM_023010.3. [Q9BZI7-2]
NP_542199.1. NM_080632.2. [Q9BZI7-1]
UniGeneiHs.103832.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UW4X-ray1.95A/C50-140[»]
2XB2X-ray3.40G/U424-483[»]
ProteinModelPortaliQ9BZI7.
SMRiQ9BZI7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122396. 44 interactors.
DIPiDIP-31143N.
IntActiQ9BZI7. 23 interactors.
MINTiMINT-265168.
STRINGi9606.ENSP00000276201.

PTM databases

iPTMnetiQ9BZI7.
PhosphoSitePlusiQ9BZI7.

Polymorphism and mutation databases

BioMutaiUPF3B.
DMDMi60390643.

Proteomic databases

EPDiQ9BZI7.
MaxQBiQ9BZI7.
PaxDbiQ9BZI7.
PeptideAtlasiQ9BZI7.
PRIDEiQ9BZI7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000276201; ENSP00000276201; ENSG00000125351. [Q9BZI7-1]
ENST00000345865; ENSP00000245418; ENSG00000125351. [Q9BZI7-2]
GeneIDi65109.
KEGGihsa:65109.
UCSCiuc004erz.3. human. [Q9BZI7-1]

Organism-specific databases

CTDi65109.
DisGeNETi65109.
GeneCardsiUPF3B.
HGNCiHGNC:20439. UPF3B.
HPAiHPA001592.
HPA001800.
HPA001882.
MalaCardsiUPF3B.
MIMi300298. gene.
300676. phenotype.
neXtProtiNX_Q9BZI7.
OpenTargetsiENSG00000125351.
Orphaneti323. FG syndrome.
776. X-linked intellectual disability with marfanoid habitus.
777. X-linked non-syndromic intellectual disability.
PharmGKBiPA128394708.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1295. Eukaryota.
ENOG41122XD. LUCA.
GeneTreeiENSGT00390000017146.
HOGENOMiHOG000230909.
HOVERGENiHBG059714.
InParanoidiQ9BZI7.
KOiK14328.
OMAiRCPEKER.
OrthoDBiEOG091G0JKF.
PhylomeDBiQ9BZI7.
TreeFamiTF316034.

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.
R-HSA-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

EvolutionaryTraceiQ9BZI7.
GeneWikiiUPF3B.
GenomeRNAii65109.
PROiQ9BZI7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000125351.
CleanExiHS_UPF3B.
ExpressionAtlasiQ9BZI7. baseline and differential.
GenevisibleiQ9BZI7. HS.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR005120. Nonsense_mediated_decay_UPF3.
IPR012677. Nucleotide-bd_a/b_plait.
[Graphical view]
PfamiPF03467. Smg4_UPF3. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiREN3B_HUMAN
AccessioniPrimary (citable) accession number: Q9BZI7
Secondary accession number(s): D3DWI3
, D3DWI4, Q0VAK8, Q9H1J0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: June 1, 2001
Last modified: November 2, 2016
This is version 140 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 X
    Human chromosome X: 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.