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Protein

U3 small nucleolar RNA-interacting protein 2

Gene

RRP9

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

Functioni

Component of a nucleolar small nuclear ribonucleoprotein particle (snoRNP) thought to participate in the processing and modification of pre-ribosomal RNA.

GO - Molecular functioni

  • RNA binding Source: UniProtKB
  • snoRNA binding Source: GO_Central
  • U3 snoRNA binding Source: InterPro

GO - Biological processi

Keywordsi

Molecular functionRibonucleoprotein, RNA-binding
Biological processrRNA processing

Enzyme and pathway databases

ReactomeiR-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
SignaLinkiO43818

Names & Taxonomyi

Protein namesi
Recommended name:
U3 small nucleolar RNA-interacting protein 2
Alternative name(s):
RRP9 homolog
U3 small nucleolar ribonucleoprotein-associated 55 kDa protein
Short name:
U3 snoRNP-associated 55 kDa protein
Short name:
U3-55K
Gene namesi
Name:RRP9
Synonyms:RNU3IP2, U355K
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000114767.6
HGNCiHGNC:16829 RRP9
neXtProtiNX_O43818

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

Pathology & Biotechi

Organism-specific databases

DisGeNETi9136
OpenTargetsiENSG00000114767
PharmGKBiPA162402176

Polymorphism and mutation databases

BioMutaiRRP9

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000513131 – 475U3 small nucleolar RNA-interacting protein 2Add BLAST475

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei10Omega-N-methylarginineCombined sources1
Modified residuei50PhosphoserineCombined sources1
Modified residuei51PhosphoserineCombined sources1
Modified residuei53PhosphoserineCombined sources1
Modified residuei57PhosphoserineCombined sources1
Cross-linki113Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiO43818
MaxQBiO43818
PaxDbiO43818
PeptideAtlasiO43818
PRIDEiO43818
ProteomicsDBi49181

2D gel databases

DOSAC-COBS-2DPAGEiO43818
SWISS-2DPAGEiO43818

PTM databases

iPTMnetiO43818
PhosphoSitePlusiO43818

Expressioni

Gene expression databases

BgeeiENSG00000114767 Expressed in 125 organ(s), highest expression level in ectocervix
CleanExiHS_RRP9
GenevisibleiO43818 HS

Organism-specific databases

HPAiHPA038798

Interactioni

Subunit structurei

Interacts specifically with the U3 small nucleolar RNA (U3 snoRNA). Binds a sub-fragment of the U3 snoRNA surrounding the B/C motif (3UBC). This association with the U3BC RNA is dependent on the binding of a protein called 15.5K to the box B/C motif. The association of the protein with the U3BC RNA was found to be also dependent on a conserved RNA structure that flanks the box B/C motif.2 Publications

Protein-protein interaction databases

BioGridi114584, 38 interactors
IntActiO43818, 10 interactors
STRINGi9606.ENSP00000232888

Structurei

Secondary structure

1475
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO43818
SMRiO43818
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati144 – 183WD 1Add BLAST40
Repeati197 – 236WD 2Add BLAST40
Repeati239 – 278WD 3Add BLAST40
Repeati281 – 320WD 4Add BLAST40
Repeati322 – 360WD 5Add BLAST39
Repeati374 – 413WD 6Add BLAST40
Repeati419 – 460WD 7Add BLAST42

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi8 – 40Nuclear localization signalSequence analysisAdd BLAST33

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi47 – 105Glu-richAdd BLAST59

Domaini

The WD domains are required for nucleolar localization and U3 small nucleolar RNAs binding.

Sequence similaritiesi

Belongs to the WD repeat RRP9 family.Curated

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0299 Eukaryota
ENOG410XP9U LUCA
GeneTreeiENSGT00910000144185
HOGENOMiHOG000188732
HOVERGENiHBG079296
InParanoidiO43818
KOiK14793
OMAiHILCMAI
OrthoDBiEOG091G0CZJ
PhylomeDBiO43818
TreeFamiTF105828

Family and domain databases

Gene3Di2.130.10.10, 1 hit
InterProiView protein in InterPro
IPR020472 G-protein_beta_WD-40_rep
IPR039241 Rrp9-like
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR019775 WD40_repeat_CS
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
PANTHERiPTHR19865 PTHR19865, 1 hit
PfamiView protein in Pfam
PF00400 WD40, 5 hits
PRINTSiPR00320 GPROTEINBRPT
SMARTiView protein in SMART
SM00320 WD40, 6 hits
SUPFAMiSSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS00678 WD_REPEATS_1, 1 hit
PS50082 WD_REPEATS_2, 5 hits
PS50294 WD_REPEATS_REGION, 1 hit

Sequencei

Sequence statusi: Complete.

O43818-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSATAAARKR GKPASGAGAG AGAGKRRRKA DSAGDRGKSK GGGKMNEEIS
60 70 80 90 100
SDSESESLAP RKPEEEEEEE LEETAQEKKL RLAKLYLEQL RQQEEEKAEA
110 120 130 140 150
RAFEEDQVAG RLKEDVLEQR GRLQKLVAKE IQAPASADIR VLRGHQLSIT
160 170 180 190 200
CLVVTPDDSA IFSAAKDCSI IKWSVESGRK LHVIPRAKKG AEGKPPGHSS
210 220 230 240 250
HVLCMAISSD GKYLASGDRS KLILIWEAQS CQHLYTFTGH RDAVSGLAFR
260 270 280 290 300
RGTHQLYSTS HDRSVKVWNV AENSYVETLF GHQDAVAALD ALSRECCVTA
310 320 330 340 350
GGRDGTVRVW KIPEESQLVF YGHQGSIDCI HLINEEHMVS GADDGSVALW
360 370 380 390 400
GLSKKRPLAL QREAHGLRGE PGLEQPFWIS SVAALLNTDL VATGSHSSCV
410 420 430 440 450
RLWQCGEGFR QLDLLCDIPL VGFINSLKFS SSGDFLVAGV GQEHRLGRWW
460 470
RIKEARNSVC IIPLRRVPVP PAAGS
Length:475
Mass (Da):51,841
Last modified:June 1, 1998 - v1
Checksum:i3CD19F66EA75B627
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0358878R → G in a breast cancer sample; somatic mutation. 1 PublicationCorresponds to variant dbSNP:rs1333637065Ensembl.1
Natural variantiVAR_035888342A → E in a breast cancer sample; somatic mutation. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ001340 mRNA Translation: CAA04687.1
AK313696 mRNA Translation: BAG36443.1
CH471055 Genomic DNA Translation: EAW65159.1
BC001113 mRNA Translation: AAH01113.1
BC009879 mRNA Translation: AAH09879.1
BC010048 mRNA Translation: AAH10048.1
BC023662 mRNA Translation: AAH23662.2
CCDSiCCDS2837.1
RefSeqiNP_004695.1, NM_004704.4
UniGeneiHs.153768

Genome annotation databases

EnsembliENST00000232888; ENSP00000232888; ENSG00000114767
GeneIDi9136
KEGGihsa:9136
UCSCiuc003dbw.3 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ001340 mRNA Translation: CAA04687.1
AK313696 mRNA Translation: BAG36443.1
CH471055 Genomic DNA Translation: EAW65159.1
BC001113 mRNA Translation: AAH01113.1
BC009879 mRNA Translation: AAH09879.1
BC010048 mRNA Translation: AAH10048.1
BC023662 mRNA Translation: AAH23662.2
CCDSiCCDS2837.1
RefSeqiNP_004695.1, NM_004704.4
UniGeneiHs.153768

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4J0WX-ray1.70A137-475[»]
4JXMX-ray1.92A118-470[»]
ProteinModelPortaliO43818
SMRiO43818
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114584, 38 interactors
IntActiO43818, 10 interactors
STRINGi9606.ENSP00000232888

PTM databases

iPTMnetiO43818
PhosphoSitePlusiO43818

Polymorphism and mutation databases

BioMutaiRRP9

2D gel databases

DOSAC-COBS-2DPAGEiO43818
SWISS-2DPAGEiO43818

Proteomic databases

EPDiO43818
MaxQBiO43818
PaxDbiO43818
PeptideAtlasiO43818
PRIDEiO43818
ProteomicsDBi49181

Protocols and materials databases

DNASUi9136
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000232888; ENSP00000232888; ENSG00000114767
GeneIDi9136
KEGGihsa:9136
UCSCiuc003dbw.3 human

Organism-specific databases

CTDi9136
DisGeNETi9136
EuPathDBiHostDB:ENSG00000114767.6
GeneCardsiRRP9
HGNCiHGNC:16829 RRP9
HPAiHPA038798
neXtProtiNX_O43818
OpenTargetsiENSG00000114767
PharmGKBiPA162402176
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0299 Eukaryota
ENOG410XP9U LUCA
GeneTreeiENSGT00910000144185
HOGENOMiHOG000188732
HOVERGENiHBG079296
InParanoidiO43818
KOiK14793
OMAiHILCMAI
OrthoDBiEOG091G0CZJ
PhylomeDBiO43818
TreeFamiTF105828

Enzyme and pathway databases

ReactomeiR-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
SignaLinkiO43818

Miscellaneous databases

ChiTaRSiRRP9 human
GeneWikiiRRP9
GenomeRNAii9136
PROiPR:O43818

Gene expression databases

BgeeiENSG00000114767 Expressed in 125 organ(s), highest expression level in ectocervix
CleanExiHS_RRP9
GenevisibleiO43818 HS

Family and domain databases

Gene3Di2.130.10.10, 1 hit
InterProiView protein in InterPro
IPR020472 G-protein_beta_WD-40_rep
IPR039241 Rrp9-like
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR019775 WD40_repeat_CS
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
PANTHERiPTHR19865 PTHR19865, 1 hit
PfamiView protein in Pfam
PF00400 WD40, 5 hits
PRINTSiPR00320 GPROTEINBRPT
SMARTiView protein in SMART
SM00320 WD40, 6 hits
SUPFAMiSSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS00678 WD_REPEATS_1, 1 hit
PS50082 WD_REPEATS_2, 5 hits
PS50294 WD_REPEATS_REGION, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiU3IP2_HUMAN
AccessioniPrimary (citable) accession number: O43818
Secondary accession number(s): B2R996, Q8IZ30
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: June 1, 1998
Last modified: November 7, 2018
This is version 163 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, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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