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Protein

Ribosomal RNA-processing protein 9

Gene

RRP9

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.1 Publication

GO - Molecular functioni

  • snoRNA binding Source: SGD

GO - Biological processi

  • rRNA methylation Source: Reactome
  • rRNA modification Source: SGD
  • rRNA processing Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Enzyme and pathway databases

BioCyciYEAST:G3O-34272-MONOMER.
ReactomeiR-SCE-6790901. rRNA modification in the nucleus.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA-processing protein 9
Gene namesi
Name:RRP9
Ordered Locus Names:YPR137W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPR137W.
SGDiS000006341. RRP9.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 573572Ribosomal RNA-processing protein 9PRO_0000269482Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources
Modified residuei50 – 501PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ06506.

PTM databases

iPTMnetiQ06506.

Interactioni

Subunit structurei

Interacts with UTP25. Component of the ribosomal small subunit (SSU) processome composed of at least 40 protein subunits and snoRNA U3.2 Publications

Protein-protein interaction databases

BioGridi36303. 56 interactions.
DIPiDIP-6537N.
IntActiQ06506. 37 interactions.
MINTiMINT-671209.

Structurei

Secondary structure

1
573
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni137 – 1393Combined sources
Beta strandi141 – 15111Combined sources
Beta strandi153 – 1553Combined sources
Beta strandi157 – 1637Combined sources
Beta strandi186 – 1916Combined sources
Beta strandi194 – 2007Combined sources
Beta strandi209 – 2157Combined sources
Helixi218 – 2203Combined sources
Beta strandi239 – 2446Combined sources
Beta strandi248 – 2558Combined sources
Beta strandi258 – 2647Combined sources
Turni265 – 2684Combined sources
Beta strandi269 – 2757Combined sources
Beta strandi283 – 2886Combined sources
Beta strandi292 – 2998Combined sources
Beta strandi302 – 3087Combined sources
Turni309 – 3124Combined sources
Beta strandi313 – 3197Combined sources
Beta strandi327 – 3293Combined sources
Beta strandi332 – 3398Combined sources
Beta strandi345 – 3506Combined sources
Turni351 – 3544Combined sources
Beta strandi355 – 3606Combined sources
Helixi365 – 3728Combined sources
Beta strandi402 – 4098Combined sources
Beta strandi412 – 4176Combined sources
Beta strandi422 – 4265Combined sources
Beta strandi433 – 4364Combined sources
Turni437 – 4404Combined sources
Beta strandi477 – 4804Combined sources
Beta strandi484 – 4907Combined sources
Beta strandi492 – 4943Combined sources
Beta strandi496 – 5016Combined sources
Beta strandi508 – 5147Combined sources
Beta strandi519 – 52810Combined sources
Beta strandi537 – 54610Combined sources
Beta strandi562 – 5698Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4J0XX-ray2.50A/B127-573[»]
ProteinModelPortaliQ06506.
SMRiQ06506. Positions 129-570.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati234 – 27340WD 1Add
BLAST
Repeati278 – 31740WD 2Add
BLAST
Repeati320 – 35940WD 3Add
BLAST
Repeati397 – 43539WD 4Add
BLAST
Repeati471 – 50939WD 5Add
BLAST
Repeati516 – 56247WD 6Add
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili32 – 10675Sequence analysisAdd
BLAST

Domaini

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

Sequence similaritiesi

Belongs to the WD repeat RRP9 family.Curated
Contains 6 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil, Repeat, WD repeat

Phylogenomic databases

GeneTreeiENSGT00840000129872.
HOGENOMiHOG000188732.
InParanoidiQ06506.
KOiK14793.
OMAiGKLYRWI.
OrthoDBiEOG7GFBDZ.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 1 hit.
[Graphical view]
SMARTiSM00320. WD40. 5 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 3 hits.
PROSITEiPS50082. WD_REPEATS_2. 1 hit.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q06506-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDVTQQKKR KRSKGEVNPS KPTVDEEITD PSSNEDEQLE VSDEEDALES
60 70 80 90 100
EEEFEGENPA DKRRRLAKQY LENLKSEAND ILTDNRNAEE KDLNNLKERT
110 120 130 140 150
IDEYNNFDAG DLDKDIIASR LKEDVAEQQG RVFRYFGDKL LISEAKQSFT
160 170 180 190 200
RVGENNLTCI SCFQPVLNKY TFEESSNGDK NKGRLFAYTV SKDLQLTKYD
210 220 230 240 250
ITDFSKRPKK LKYAKGGAKY IPTSKHEYEN TTEGHYDEIL TVAASPDGKY
260 270 280 290 300
VVTGGRDRKL IVWSTESLSP VKVIPTKDRR GEVLSLAFRK NSDQLYASCA
310 320 330 340 350
DFKIRTYSIN QFSQLEILYG HHDIVEDISA LAMERCVTVG ARDRTAMLWK
360 370 380 390 400
IPDETRLTFR GGDEPQKLLR RWMKENAKEG EDGEVKYPDE SEAPLFFCEG
410 420 430 440 450
SIDVVSMVDD FHFITGSDNG NICLWSLAKK KPIFTERIAH GILPEPSFND
460 470 480 490 500
ISGETDEELR KRQLQGKKLL QPFWITSLYA IPYSNVFISG SWSGSLKVWK
510 520 530 540 550
ISDNLRSFEL LGELSGAKGV VTKIQVVESG KHGKEKFRIL ASIAKEHRLG
560 570
RWIANVSGAR NGIYSAVIDQ TGF
Length:573
Mass (Da):65,054
Last modified:November 1, 1996 - v1
Checksum:i96BEAB7DC338E70E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U40829 Genomic DNA. Translation: AAB68277.1.
BK006949 Genomic DNA. Translation: DAA11549.1.
PIRiS69026.
RefSeqiNP_015463.1. NM_001184234.1.

Genome annotation databases

EnsemblFungiiYPR137W; YPR137W; YPR137W.
GeneIDi856255.
KEGGisce:YPR137W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U40829 Genomic DNA. Translation: AAB68277.1.
BK006949 Genomic DNA. Translation: DAA11549.1.
PIRiS69026.
RefSeqiNP_015463.1. NM_001184234.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4J0XX-ray2.50A/B127-573[»]
ProteinModelPortaliQ06506.
SMRiQ06506. Positions 129-570.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36303. 56 interactions.
DIPiDIP-6537N.
IntActiQ06506. 37 interactions.
MINTiMINT-671209.

PTM databases

iPTMnetiQ06506.

Proteomic databases

MaxQBiQ06506.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPR137W; YPR137W; YPR137W.
GeneIDi856255.
KEGGisce:YPR137W.

Organism-specific databases

EuPathDBiFungiDB:YPR137W.
SGDiS000006341. RRP9.

Phylogenomic databases

GeneTreeiENSGT00840000129872.
HOGENOMiHOG000188732.
InParanoidiQ06506.
KOiK14793.
OMAiGKLYRWI.
OrthoDBiEOG7GFBDZ.

Enzyme and pathway databases

BioCyciYEAST:G3O-34272-MONOMER.
ReactomeiR-SCE-6790901. rRNA modification in the nucleus.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus.

Miscellaneous databases

PROiQ06506.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 1 hit.
[Graphical view]
SMARTiSM00320. WD40. 5 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 3 hits.
PROSITEiPS50082. WD_REPEATS_2. 1 hit.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Yeast Rrp9p is an evolutionarily conserved U3 snoRNP protein essential for early pre-rRNA processing cleavages and requires box C for its association."
    Venema J., Vos H.R., Faber A.W., van Venrooij W.J., Raue H.A.
    RNA 6:1660-1671(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ASSOCIATION WITH U3 SNORNA.
  4. Cited for: IDENTIFICATION IN SSU PROCESSOME BY MASS SPECTROMETRY.
  5. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "The DEAD-box RNA helicase-like Utp25 is an SSU processome component."
    Charette J.M., Baserga S.J.
    RNA 16:2156-2169(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH UTP25.
  9. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRRP9_YEAST
AccessioniPrimary (citable) accession number: Q06506
Secondary accession number(s): D6W4D3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 12, 2006
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 131 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 5130 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

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.