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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
  • meiotic chromosome segregation Source: PomBase
  • meiotic telomere clustering 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
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000514971 – 638Rik1-associated factor 1Add BLAST638

Proteomic databases

MaxQBiO74910.
PRIDEiO74910.

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 interactors.
DIPiDIP-37644N.
IntActiO74910. 6 interactors.
MINTiMINT-4681782.

Structurei

Secondary structure

1638
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi226 – 228Combined sources3
Beta strandi231 – 236Combined sources6
Beta strandi243 – 248Combined sources6
Beta strandi252 – 259Combined sources8
Beta strandi271 – 276Combined sources6
Turni277 – 280Combined sources4
Beta strandi281 – 284Combined sources4
Beta strandi289 – 291Combined sources3
Beta strandi297 – 299Combined sources3
Beta strandi302 – 307Combined sources6
Beta strandi311 – 318Combined sources8
Beta strandi323 – 327Combined sources5
Beta strandi332 – 336Combined sources5
Beta strandi343 – 348Combined sources6
Beta strandi354 – 358Combined sources5
Beta strandi363 – 368Combined sources6
Turni370 – 372Combined sources3
Beta strandi375 – 381Combined sources7
Helixi384 – 388Combined sources5
Beta strandi392 – 399Combined sources8
Turni401 – 404Combined sources4
Beta strandi408 – 414Combined sources7
Beta strandi424 – 429Combined sources6
Turni430 – 433Combined sources4
Beta strandi434 – 438Combined sources5
Beta strandi445 – 451Combined sources7
Beta strandi456 – 463Combined sources8
Beta strandi465 – 474Combined sources10
Turni475 – 478Combined sources4
Beta strandi479 – 487Combined sources9
Beta strandi489 – 496Combined sources8
Beta strandi502 – 507Combined sources6
Beta strandi510 – 516Combined sources7
Beta strandi524 – 528Combined sources5
Beta strandi551 – 554Combined sources4
Beta strandi561 – 564Combined sources4
Beta strandi568 – 573Combined sources6
Beta strandi577 – 579Combined sources3
Beta strandi581 – 587Combined sources7
Beta strandi592 – 597Combined sources6
Beta strandi601 – 608Combined sources8
Beta strandi613 – 617Combined sources5
Beta strandi630 – 632Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4O9DX-ray2.00A/B213-638[»]
ProteinModelPortaliO74910.
SMRiO74910.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati297 – 336WD 1Add BLAST40
Repeati486 – 525WD 2Add BLAST40
Repeati544 – 583WD 3Add BLAST40
Repeati587 – 626WD 4Add BLAST40

Sequence similaritiesi

Contains 4 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

InParanoidiO74910.
OrthoDBiEOG092C1PD4.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4O9DX-ray2.00A/B213-638[»]
ProteinModelPortaliO74910.
SMRiO74910.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi275429. 254 interactors.
DIPiDIP-37644N.
IntActiO74910. 6 interactors.
MINTiMINT-4681782.

Proteomic databases

MaxQBiO74910.
PRIDEiO74910.

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.
OrthoDBiEOG092C1PD4.
PhylomeDBiO74910.

Miscellaneous databases

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...

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: November 2, 2016
This is version 120 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.