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Protein

U3 small nucleolar RNA-interacting protein 2

Gene

RRP9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • rRNA processing Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000114767-MONOMER.
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

HGNCiHGNC:16829. RRP9.

Subcellular locationi

GO - Cellular componenti

  • box C/D snoRNP complex Source: UniProtKB
  • nucleolus Source: GO_Central
  • nucleoplasm Source: Reactome
  • nucleus Source: HPA
  • small-subunit processome Source: GO_Central
Complete GO annotation...

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

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiO43818.
MaxQBiO43818.
PaxDbiO43818.
PeptideAtlasiO43818.
PRIDEiO43818.

2D gel databases

DOSAC-COBS-2DPAGEO43818.
SWISS-2DPAGEO43818.

PTM databases

iPTMnetiO43818.
PhosphoSitePlusiO43818.

Expressioni

Gene expression databases

BgeeiENSG00000114767.
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. 35 interactors.
IntActiO43818. 8 interactors.
MINTiMINT-2999726.
STRINGi9606.ENSP00000232888.

Structurei

Secondary structure

1475
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni136 – 138Combined sources3
Beta strandi140 – 143Combined sources4
Beta strandi149 – 154Combined sources6
Beta strandi158 – 165Combined sources8
Beta strandi170 – 174Combined sources5
Turni175 – 177Combined sources3
Beta strandi180 – 184Combined sources5
Beta strandi202 – 207Combined sources6
Beta strandi213 – 218Combined sources6
Beta strandi223 – 227Combined sources5
Turni228 – 231Combined sources4
Beta strandi232 – 237Combined sources6
Beta strandi244 – 249Combined sources6
Beta strandi253 – 260Combined sources8
Beta strandi263 – 269Combined sources7
Helixi270 – 272Combined sources3
Beta strandi274 – 280Combined sources7
Beta strandi288 – 291Combined sources4
Beta strandi293 – 300Combined sources8
Beta strandi306 – 311Combined sources6
Turni312 – 315Combined sources4
Beta strandi316 – 321Combined sources6
Beta strandi323 – 325Combined sources3
Beta strandi327 – 334Combined sources8
Beta strandi337 – 342Combined sources6
Beta strandi347 – 353Combined sources7
Beta strandi358 – 361Combined sources4
Turni362 – 365Combined sources4
Beta strandi367 – 370Combined sources4
Beta strandi381 – 384Combined sources4
Beta strandi388 – 394Combined sources7
Beta strandi396 – 405Combined sources10
Helixi407 – 409Combined sources3
Beta strandi412 – 419Combined sources8
Beta strandi422 – 429Combined sources8
Beta strandi431 – 443Combined sources13
Beta strandi458 – 463Combined sources6

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...

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
Contains 7 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0299. Eukaryota.
ENOG410XP9U. LUCA.
GeneTreeiENSGT00860000133882.
HOGENOMiHOG000188732.
HOVERGENiHBG079296.
InParanoidiO43818.
KOiK14793.
OMAiAITGLDC.
OrthoDBiEOG091G0CZJ.
PhylomeDBiO43818.
TreeFamiTF105828.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 5 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 6 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 1 hit.
PS50082. WD_REPEATS_2. 5 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

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 Publication1
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

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. 35 interactors.
IntActiO43818. 8 interactors.
MINTiMINT-2999726.
STRINGi9606.ENSP00000232888.

PTM databases

iPTMnetiO43818.
PhosphoSitePlusiO43818.

Polymorphism and mutation databases

BioMutaiRRP9.

2D gel databases

DOSAC-COBS-2DPAGEO43818.
SWISS-2DPAGEO43818.

Proteomic databases

EPDiO43818.
MaxQBiO43818.
PaxDbiO43818.
PeptideAtlasiO43818.
PRIDEiO43818.

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.
GeneCardsiRRP9.
HGNCiHGNC:16829. RRP9.
HPAiHPA038798.
neXtProtiNX_O43818.
OpenTargetsiENSG00000114767.
PharmGKBiPA162402176.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0299. Eukaryota.
ENOG410XP9U. LUCA.
GeneTreeiENSGT00860000133882.
HOGENOMiHOG000188732.
HOVERGENiHBG079296.
InParanoidiO43818.
KOiK14793.
OMAiAITGLDC.
OrthoDBiEOG091G0CZJ.
PhylomeDBiO43818.
TreeFamiTF105828.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000114767-MONOMER.
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.
PROiO43818.

Gene expression databases

BgeeiENSG00000114767.
CleanExiHS_RRP9.
GenevisibleiO43818. HS.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 5 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 6 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 1 hit.
PS50082. WD_REPEATS_2. 5 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiU3IP2_HUMAN
AccessioniPrimary (citable) accession number: O43818
Secondary accession number(s): B2R996, Q8IZ30
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: June 1, 1998
Last modified: November 30, 2016
This is version 147 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. 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.