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Protein

Rik1-associated factor 1

Gene

raf1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the rik1-associated E3 ubiquitin ligase complex that shows ubiquitin ligase activity and is required for histone H3K9 methylation. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting swi6/HP1 to methylated histones which leads to transcriptional silencing within centromeric heterochromatin, telomeric regions and at the silent mating-type loci. Has a role in both mitotic and meiotic chromosome segregation.3 Publications

GO - Biological processi

  • cellular protein localization Source: PomBase
  • chromatin modification Source: UniProtKB-KW
  • chromatin silencing at centromere Source: PomBase
  • chromatin silencing at centromere outer repeat region Source: PomBase
  • chromatin silencing at silent mating-type cassette Source: PomBase
  • chromatin silencing at telomere Source: PomBase
  • chromatin silencing by small RNA Source: PomBase
  • maintenance of chromatin silencing at silent mating-type cassette Source: PomBase
  • meiotic chromosome segregation Source: PomBase
  • meiotic sister chromatid cohesion, centromeric Source: PomBase
  • meiotic telomere clustering Source: PomBase
  • mitotic sister chromatid segregation Source: PomBase
  • negative regulation of histone H3-K4 methylation Source: PomBase
  • negative regulation of transcription from RNA polymerase II promoter Source: PomBase
  • positive regulation of histone H3-K9 methylation Source: PomBase
  • regulation of mating type switching Source: PomBase
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Biological processi

Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Rik1-associated factor 1
Alternative name(s):
Cryptic loci regulator 8
De-localization of swi6 protein 1
Gene namesi
Name:raf1
Synonyms:clr8, cmc1, dos1
ORF Names:SPCC613.12c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:SPCC613.12c.
PomBaseiSPCC613.12c. raf1.

Subcellular locationi

GO - Cellular componenti

  • chromosome, centromeric outer repeat region Source: GOC
  • chromosome, telomeric region Source: GOC
  • CLRC ubiquitin ligase complex Source: PomBase
  • cytosol Source: PomBase
  • mating-type region heterochromatin Source: PomBase
  • nuclear pericentric heterochromatin Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 638638Rik1-associated factor 1PRO_0000051497Add
BLAST

Proteomic databases

MaxQBiO74910.

Interactioni

Subunit structurei

Component of the rik1-associated E3 ubiquitin ligase complex composed of at least clr4, cul4, pip1, raf1 and raf2. Interacts with nup189.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
lid2Q9HDV42EBI-904913,EBI-2105919
rik1Q104263EBI-904913,EBI-1111936
SPBP8B7.28cO942762EBI-904913,EBI-2651917

Protein-protein interaction databases

BioGridi275429. 254 interactions.
IntActiO74910. 6 interactions.
MINTiMINT-4681782.

Structurei

Secondary structure

1
638
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi226 – 2283Combined sources
Beta strandi231 – 2366Combined sources
Beta strandi243 – 2486Combined sources
Beta strandi252 – 2598Combined sources
Beta strandi271 – 2766Combined sources
Turni277 – 2804Combined sources
Beta strandi281 – 2844Combined sources
Beta strandi289 – 2913Combined sources
Beta strandi297 – 2993Combined sources
Beta strandi302 – 3076Combined sources
Beta strandi311 – 3188Combined sources
Beta strandi323 – 3275Combined sources
Beta strandi332 – 3365Combined sources
Beta strandi343 – 3486Combined sources
Beta strandi354 – 3585Combined sources
Beta strandi363 – 3686Combined sources
Turni370 – 3723Combined sources
Beta strandi375 – 3817Combined sources
Helixi384 – 3885Combined sources
Beta strandi392 – 3998Combined sources
Turni401 – 4044Combined sources
Beta strandi408 – 4147Combined sources
Beta strandi424 – 4296Combined sources
Turni430 – 4334Combined sources
Beta strandi434 – 4385Combined sources
Beta strandi445 – 4517Combined sources
Beta strandi456 – 4638Combined sources
Beta strandi465 – 47410Combined sources
Turni475 – 4784Combined sources
Beta strandi479 – 4879Combined sources
Beta strandi489 – 4968Combined sources
Beta strandi502 – 5076Combined sources
Beta strandi510 – 5167Combined sources
Beta strandi524 – 5285Combined sources
Beta strandi551 – 5544Combined sources
Beta strandi561 – 5644Combined sources
Beta strandi568 – 5736Combined sources
Beta strandi577 – 5793Combined sources
Beta strandi581 – 5877Combined sources
Beta strandi592 – 5976Combined sources
Beta strandi601 – 6088Combined sources
Beta strandi613 – 6175Combined sources
Beta strandi630 – 6323Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4O9DX-ray2.00A/B213-638[»]
ProteinModelPortaliO74910.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati297 – 33640WD 1Add
BLAST
Repeati486 – 52540WD 2Add
BLAST
Repeati544 – 58340WD 3Add
BLAST
Repeati587 – 62640WD 4Add
BLAST

Sequence similaritiesi

Contains 4 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

InParanoidiO74910.
OrthoDBiEOG70S7DT.
PhylomeDBiO74910.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
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. 2 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 5 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 2 hits.
PROSITEiPS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 2 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O74910-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTNSSPRVKR RTDTQYLHSV SSKLPKVDFD TNNEEFFEEE FEIYDPFYRA
60 70 80 90 100
ELPCPKPSLS ISKHSIAKVP SNVNKRLELQ LLLTSGTFLP NSRPYLSERV
110 120 130 140 150
RKHTHLLSNS ITGDDKPSLI HVDFTPEECF ILQEAKLKFG PVNSVQFNDA
160 170 180 190 200
YSTHISPKLP GRAYEDCQKF EIDNPSLSPV DKHGAIILRT YKKNKKLLPD
210 220 230 240 250
YLKSFYNAGS SYFQREQVHQ LMDGESVFFL KPWKHFNETS GDTVCVAYNP
260 270 280 290 300
LCEKFALGST AQDGAYNRLG NLWIGDFHSE TIQSLESHYK LNQVGEKEYS
310 320 330 340 350
TISDLCFSKG NLFLYTGAFD NAVKVWDMEG NLCGIFNAPT DYIHKLALSD
360 370 380 390 400
DDLLAVACKN GYGYLLSTDN STGEILTSAN LIYPEALEKG YSASLIEFSN
410 420 430 440 450
FLGRSSDKVI IGYDSFHTSN NRGCLALFDA STASFVQKFN TADEAFTSLY
460 470 480 490 500
MHPSQVGFVA SSNTLSNGRV YYLDTRMYKV CLNFTTTQKD INHATISNSG
510 520 530 540 550
ILVTSSGTDN QTFVWDSRKP DKPLSLLKHG KTKMIHFDGA NEEEVDAGIN
560 570 580 590 600
MAQWQPKGNL FVTGGSDGIV KVWDLRLNNP FIQNFTEMNS AITYGGFSED
610 620 630
ASKLTVCCVG GDVNMYSLGN DNGNKFGEFR IIENRLLT
Length:638
Mass (Da):71,536
Last modified:November 1, 1998 - v1
Checksum:i6CD360D8748AAF98
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329672 Genomic DNA. Translation: CAA21064.1.
PIRiT41478.
RefSeqiNP_587700.1. NM_001022695.2.

Genome annotation databases

EnsemblFungiiSPCC613.12c.1; SPCC613.12c.1:pep; SPCC613.12c.
GeneIDi2538848.
KEGGispo:SPCC613.12c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329672 Genomic DNA. Translation: CAA21064.1.
PIRiT41478.
RefSeqiNP_587700.1. NM_001022695.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4O9DX-ray2.00A/B213-638[»]
ProteinModelPortaliO74910.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi275429. 254 interactions.
IntActiO74910. 6 interactions.
MINTiMINT-4681782.

Proteomic databases

MaxQBiO74910.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPCC613.12c.1; SPCC613.12c.1:pep; SPCC613.12c.
GeneIDi2538848.
KEGGispo:SPCC613.12c.

Organism-specific databases

EuPathDBiFungiDB:SPCC613.12c.
PomBaseiSPCC613.12c. raf1.

Phylogenomic databases

InParanoidiO74910.
OrthoDBiEOG70S7DT.
PhylomeDBiO74910.

Miscellaneous databases

NextBioi20800030.
PROiO74910.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
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. 2 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 5 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 2 hits.
PROSITEiPS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 2 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation."
    Horn P.J., Bastie J.-N., Peterson C.L.
    Genes Dev. 19:1705-1714(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE, FUNCTION, IDENTIFICATION IN THE RIK1-ASSOCIATED E3 UBIQUITIN LIGASE COMPLEX, SUBCELLULAR LOCATION.
  3. "Two novel proteins, dos1 and dos2, interact with rik1 to regulate heterochromatic RNA interference and histone modification."
    Li F., Goto D.B., Zaratiegui M., Tang X., Martienssen R., Cande W.Z.
    Curr. Biol. 15:1448-1457(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RIK1, SUBCELLULAR LOCATION.
  4. "The Clr7 and Clr8 directionality factors and the Pcu4 cullin mediate heterochromatin formation in the fission yeast Schizosaccharomyces pombe."
    Thon G., Hansen K.R., Altes S.P., Sidhu D., Singh G., Verhein-Hansen J., Bonaduce M.J., Klar A.J.
    Genetics 171:1583-1595(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH NUP189.
  5. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
    Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
    Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRAF1_SCHPO
AccessioniPrimary (citable) accession number: O74910
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 14, 2001
Last sequence update: November 1, 1998
Last modified: February 17, 2016
This is version 115 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  3. 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.