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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

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
  • nucleus Source: HPA
  • small-subunit processome Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA162402176.

Polymorphism and mutation databases

BioMutaiRRP9.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 475475U3 small nucleolar RNA-interacting protein 2PRO_0000051313Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei50 – 501PhosphoserineCombined sources
Modified residuei51 – 511PhosphoserineCombined sources
Modified residuei53 – 531PhosphoserineCombined sources
Modified residuei57 – 571PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiO43818.
MaxQBiO43818.
PaxDbiO43818.
PeptideAtlasiO43818.
PRIDEiO43818.

2D gel databases

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

PTM databases

iPTMnetiO43818.
PhosphoSiteiO43818.

Expressioni

Gene expression databases

BgeeiO43818.
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 interactions.
IntActiO43818. 8 interactions.
MINTiMINT-2999726.
STRINGi9606.ENSP00000232888.

Structurei

Secondary structure

1
475
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni136 – 1383Combined sources
Beta strandi140 – 1434Combined sources
Beta strandi149 – 1546Combined sources
Beta strandi158 – 1658Combined sources
Beta strandi170 – 1745Combined sources
Turni175 – 1773Combined sources
Beta strandi180 – 1845Combined sources
Beta strandi202 – 2076Combined sources
Beta strandi213 – 2186Combined sources
Beta strandi223 – 2275Combined sources
Turni228 – 2314Combined sources
Beta strandi232 – 2376Combined sources
Beta strandi244 – 2496Combined sources
Beta strandi253 – 2608Combined sources
Beta strandi263 – 2697Combined sources
Helixi270 – 2723Combined sources
Beta strandi274 – 2807Combined sources
Beta strandi288 – 2914Combined sources
Beta strandi293 – 3008Combined sources
Beta strandi306 – 3116Combined sources
Turni312 – 3154Combined sources
Beta strandi316 – 3216Combined sources
Beta strandi323 – 3253Combined sources
Beta strandi327 – 3348Combined sources
Beta strandi337 – 3426Combined sources
Beta strandi347 – 3537Combined sources
Beta strandi358 – 3614Combined sources
Turni362 – 3654Combined sources
Beta strandi367 – 3704Combined sources
Beta strandi381 – 3844Combined sources
Beta strandi388 – 3947Combined sources
Beta strandi396 – 40510Combined sources
Helixi407 – 4093Combined sources
Beta strandi412 – 4198Combined sources
Beta strandi422 – 4298Combined sources
Beta strandi431 – 44313Combined sources
Beta strandi458 – 4636Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4J0WX-ray1.70A137-475[»]
4JXMX-ray1.92A118-470[»]
ProteinModelPortaliO43818.
SMRiO43818. Positions 87-465.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati144 – 18340WD 1Add
BLAST
Repeati197 – 23640WD 2Add
BLAST
Repeati239 – 27840WD 3Add
BLAST
Repeati281 – 32040WD 4Add
BLAST
Repeati322 – 36039WD 5Add
BLAST
Repeati374 – 41340WD 6Add
BLAST
Repeati419 – 46042WD 7Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi8 – 4033Nuclear localization signalSequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi47 – 10559Glu-richAdd
BLAST

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.
GeneTreeiENSGT00840000129872.
HOGENOMiHOG000188732.
HOVERGENiHBG079296.
InParanoidiO43818.
KOiK14793.
OMAiAITGLDC.
OrthoDBiEOG73BVCQ.
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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti8 – 81R → G in a breast cancer sample; somatic mutation. 1 Publication
VAR_035887
Natural varianti342 – 3421A → E in a breast cancer sample; somatic mutation. 1 Publication
VAR_035888

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
EntryMethodResolution (Å)ChainPositionsPDBsum
4J0WX-ray1.70A137-475[»]
4JXMX-ray1.92A118-470[»]
ProteinModelPortaliO43818.
SMRiO43818. Positions 87-465.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114584. 35 interactions.
IntActiO43818. 8 interactions.
MINTiMINT-2999726.
STRINGi9606.ENSP00000232888.

PTM databases

iPTMnetiO43818.
PhosphoSiteiO43818.

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

Phylogenomic databases

eggNOGiKOG0299. Eukaryota.
ENOG410XP9U. LUCA.
GeneTreeiENSGT00840000129872.
HOGENOMiHOG000188732.
HOVERGENiHBG079296.
InParanoidiO43818.
KOiK14793.
OMAiAITGLDC.
OrthoDBiEOG73BVCQ.
PhylomeDBiO43818.
TreeFamiTF105828.

Enzyme and pathway databases

SignaLinkiO43818.

Miscellaneous databases

ChiTaRSiRRP9. human.
GeneWikiiRRP9.
GenomeRNAii9136.
NextBioi34259.
PROiO43818.

Gene expression databases

BgeeiO43818.
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...

Publicationsi

« Hide 'large scale' publications
  1. "cDNA cloning and characterization of the human U3 small nucleolar ribonucleoprotein complex-associated 55-kilodalton protein."
    Pluk H., Soffner J., Luehrmann R., van Venrooij W.J.
    Mol. Cell. Biol. 18:488-498(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 102-113 AND 267-273.
    Tissue: Teratocarcinoma.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain and Skin.
  5. "Interaction of the U3-55k protein with U3 snoRNA is mediated by the box B/C motif of U3 and the WD repeats of U3-55k."
    Lukowiak A.A., Granneman S., Mattox S.A., Speckmann W.A., Jones K., Pluk H., van Venrooij W.J., Terns R.M., Terns M.P.
    Nucleic Acids Res. 28:3462-3471(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH U3 SNRNA.
  6. "The hU3-55K protein requires 15.5K binding to the box B/C motif as well as flanking RNA elements for its association with the U3 small nucleolar RNA in Vitro."
    Granneman S., Pruijn G.J.M., Horstman W., van Venrooij W.J., Luehrmann R., Watkins N.J.
    J. Biol. Chem. 277:48490-48500(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH U3 SNRNA.
  7. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  8. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50; SER-51; SER-53 AND SER-57, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50; SER-51 AND SER-53, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  10. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50; SER-51 AND SER-53, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Crystal structure of RRP9 WD40 repeats."
    Structural genomics consortium (SGC)
    Submitted (APR-2013) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) OF 118-470.
  12. Cited for: VARIANTS [LARGE SCALE ANALYSIS] GLY-8 AND GLU-342.

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: May 11, 2016
This is version 142 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.