RAP1_YEAST
ID RAP1_YEAST Reviewed; 827 AA.
AC P11938; D6W0X4;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 2.
DT 03-AUG-2022, entry version 217.
DE RecName: Full=DNA-binding protein RAP1;
DE AltName: Full=Repressor/activator site-binding protein;
DE AltName: Full=SBF-E;
DE AltName: Full=TUF;
GN Name=RAP1; Synonyms=GRF1, TUF1; OrderedLocusNames=YNL216W; ORFNames=N1310;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=BJ2168;
RX PubMed=3315231; DOI=10.1016/0092-8674(87)90095-x;
RA Shore D., Nasmyth K.;
RT "Purification and cloning of a DNA binding protein from yeast that binds to
RT both silencer and activator elements.";
RL Cell 51:721-732(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=7762305; DOI=10.1002/yea.320110111;
RA Coster F., van Dyck L., Jonniaux J.-L., Purnelle B., Goffeau A.;
RT "The sequence of a 13.5 kb DNA segment from the left arm of yeast
RT chromosome XIV reveals MER1; RAP1; a new putative member of the DNA
RT replication complex and a new putative serine/threonine phosphatase gene.";
RL Yeast 11:85-91(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(1997).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP INTERACTION WITH GCR1.
RX PubMed=8508768; DOI=10.1002/j.1460-2075.1993.tb05897.x;
RA Tornow J., Zeng X., Gao W., Santangelo G.M.;
RT "GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes
RT with RAP1 and can function without its DNA binding domain.";
RL EMBO J. 12:2431-2437(1993).
RN [6]
RP CHARACTERIZATION.
RX PubMed=8194531; DOI=10.1002/j.1460-2075.1994.tb06526.x;
RA Giraldo R., Rhodes D.;
RT "The yeast telomere-binding protein RAP1 binds to and promotes the
RT formation of DNA quadruplexes in telomeric DNA.";
RL EMBO J. 13:2411-2420(1994).
RN [7]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-486, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-731, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF 360-600.
RX PubMed=8620531; DOI=10.1016/s0092-8674(00)81088-0;
RA Koenig P., Giraldo R., Chapman L., Rhodes D.;
RT "The crystal structure of the DNA-binding domain of yeast RAP1 in complex
RT with telomeric DNA.";
RL Cell 85:125-136(1996).
CC -!- FUNCTION: Essential regulatory protein in yeast whose DNA-binding sites
CC are found at three types of chromosomal elements: promoters, silencers,
CC and telomeres. RAP1 is also involved in the regulation of telomere
CC structure, where its binding sites are found within the terminal
CC poly[C(1-3)A] sequences. The opposite regulatory functions of RAP1 are
CC not intrinsic to its binding sites but, instead, result from
CC interactions with different factors at promoters and silencers. RAP1
CC associates with SIR3 and SIR4 proteins to form a DNA-binding complex
CC that initiates the repression at the HM loci and telomeres. May also
CC target the binding of RIF1 and RIF2 to silencers and telomeres. Forms
CC with GCR1 a transcriptional activation complex that is required for
CC expression of glycolytic and ribosomal gene.
CC -!- SUBUNIT: RIF1, SIR3 and SIR4 associate with RAP1 C-terminus in vivo.
CC Interacts with a GCR1 homodimer. {ECO:0000269|PubMed:8508768}.
CC -!- INTERACTION:
CC P11938; Q08649: ESA1; NbExp=6; IntAct=EBI-14821, EBI-6648;
CC P11938; P03069: GCN4; NbExp=5; IntAct=EBI-14821, EBI-7450;
CC P11938; P07261: GCR1; NbExp=2; IntAct=EBI-14821, EBI-7463;
CC P11938; P29539: RIF1; NbExp=3; IntAct=EBI-14821, EBI-2083307;
CC P11938; Q06208: RIF2; NbExp=5; IntAct=EBI-14821, EBI-15199;
CC P11938; P06701: SIR3; NbExp=8; IntAct=EBI-14821, EBI-17230;
CC P11938; P11978: SIR4; NbExp=4; IntAct=EBI-14821, EBI-17237;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q96TL7}.
CC Chromosome, telomere {ECO:0000250|UniProtKB:Q96TL7}.
CC -!- MISCELLANEOUS: Present with 4390 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RAP1 family. {ECO:0000305}.
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DR EMBL; M18068; AAA18404.1; -; Unassigned_DNA.
DR EMBL; X78898; CAA55491.1; -; Genomic_DNA.
DR EMBL; Z71492; CAA96118.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10340.1; -; Genomic_DNA.
DR PIR; S50714; S50714.
DR RefSeq; NP_014183.1; NM_001183054.1.
DR PDB; 1IGN; X-ray; 2.25 A; A/B=353-598.
DR PDB; 2L42; NMR; -; A=116-212.
DR PDB; 3CZ6; X-ray; 1.85 A; A/B=672-827.
DR PDB; 3OWT; X-ray; 2.00 A; A/B=672-827.
DR PDB; 3UKG; X-ray; 2.95 A; A=360-601.
DR PDB; 4BJ5; X-ray; 3.29 A; C/E=627-827.
DR PDB; 4BJ6; X-ray; 3.26 A; C/E=627-827.
DR PDB; 4BJT; X-ray; 1.61 A; A/B/C=627-827.
DR PDB; 4GFB; X-ray; 2.99 A; A=358-602.
DR PDB; 6LDM; X-ray; 2.40 A; A=353-598.
DR PDBsum; 1IGN; -.
DR PDBsum; 2L42; -.
DR PDBsum; 3CZ6; -.
DR PDBsum; 3OWT; -.
DR PDBsum; 3UKG; -.
DR PDBsum; 4BJ5; -.
DR PDBsum; 4BJ6; -.
DR PDBsum; 4BJT; -.
DR PDBsum; 4GFB; -.
DR PDBsum; 6LDM; -.
DR AlphaFoldDB; P11938; -.
DR BMRB; P11938; -.
DR SMR; P11938; -.
DR BioGRID; 35620; 706.
DR ComplexPortal; CPX-1200; RAP1-GCR1 transcription activation complex.
DR ComplexPortal; CPX-1229; RAP1-GCR1-GCR2 transcription activation complex.
DR ComplexPortal; CPX-2112; Telosome.
DR DIP; DIP-851N; -.
DR IntAct; P11938; 50.
DR MINT; P11938; -.
DR STRING; 4932.YNL216W; -.
DR iPTMnet; P11938; -.
DR MaxQB; P11938; -.
DR PaxDb; P11938; -.
DR PRIDE; P11938; -.
DR EnsemblFungi; YNL216W_mRNA; YNL216W; YNL216W.
DR GeneID; 855505; -.
DR KEGG; sce:YNL216W; -.
DR SGD; S000005160; RAP1.
DR VEuPathDB; FungiDB:YNL216W; -.
DR eggNOG; ENOG502S85C; Eukaryota.
DR HOGENOM; CLU_014729_0_0_1; -.
DR InParanoid; P11938; -.
DR OMA; EISHYVP; -.
DR BioCyc; YEAST:G3O-33222-MON; -.
DR EvolutionaryTrace; P11938; -.
DR PRO; PR:P11938; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P11938; protein.
DR GO; GO:0000781; C:chromosome, telomeric region; IDA:SGD.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0000228; C:nuclear chromosome; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0032993; C:protein-DNA complex; IMP:CAFA.
DR GO; GO:0070187; C:shelterin complex; IDA:SGD.
DR GO; GO:0005667; C:transcription regulator complex; IPI:ComplexPortal.
DR GO; GO:0000987; F:cis-regulatory region sequence-specific DNA binding; IDA:SGD.
DR GO; GO:0008301; F:DNA binding, bending; IDA:SGD.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:SGD.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IDA:SGD.
DR GO; GO:0003691; F:double-stranded telomeric DNA binding; IMP:CAFA.
DR GO; GO:0051880; F:G-quadruplex DNA binding; IDA:SGD.
DR GO; GO:0042393; F:histone binding; IDA:SGD.
DR GO; GO:0031492; F:nucleosomal DNA binding; IDA:SGD.
DR GO; GO:0061629; F:RNA polymerase II-specific DNA-binding transcription factor binding; IDA:SGD.
DR GO; GO:0043565; F:sequence-specific DNA binding; HDA:SGD.
DR GO; GO:0017025; F:TBP-class protein binding; IDA:SGD.
DR GO; GO:0042162; F:telomeric DNA binding; IDA:SGD.
DR GO; GO:0001094; F:TFIID-class transcription factor complex binding; IDA:SGD.
DR GO; GO:0071169; P:establishment of protein localization to chromatin; IPI:SGD.
DR GO; GO:0070200; P:establishment of protein localization to telomere; IPI:SGD.
DR GO; GO:0071919; P:G-quadruplex DNA formation; IDA:CACAO.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0060963; P:positive regulation of ribosomal protein gene transcription by RNA polymerase II; IC:ComplexPortal.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0031848; P:protection from non-homologous end joining at telomere; IMP:SGD.
DR GO; GO:0006110; P:regulation of glycolytic process; IC:ComplexPortal.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0030466; P:silent mating-type cassette heterochromatin assembly; IGI:SGD.
DR GO; GO:0031509; P:subtelomeric heterochromatin assembly; IGI:SGD.
DR GO; GO:0000723; P:telomere maintenance; IMP:SGD.
DR GO; GO:0010833; P:telomere maintenance via telomere lengthening; IDA:SGD.
DR DisProt; DP00020; -.
DR Gene3D; 1.10.10.2170; -; 1.
DR Gene3D; 3.40.50.10190; -; 1.
DR IDEAL; IID50071; -.
DR InterPro; IPR001357; BRCT_dom.
DR InterPro; IPR036420; BRCT_dom_sf.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017930; Myb_dom.
DR InterPro; IPR021661; Rap1_C.
DR InterPro; IPR038104; Rap1_C_sf.
DR InterPro; IPR015280; Rap1_DNA-bd.
DR InterPro; IPR001005; SANT/Myb.
DR InterPro; IPR039595; TE2IP/Rap1.
DR PANTHER; PTHR16466; PTHR16466; 1.
DR Pfam; PF16589; BRCT_2; 1.
DR Pfam; PF00249; Myb_DNA-binding; 1.
DR Pfam; PF09197; Rap1-DNA-bind; 1.
DR Pfam; PF11626; Rap1_C; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM00717; SANT; 1.
DR SUPFAM; SSF46689; SSF46689; 2.
DR SUPFAM; SSF52113; SSF52113; 1.
DR PROSITE; PS50172; BRCT; 1.
DR PROSITE; PS51294; HTH_MYB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Activator; Chromosome; DNA-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Repressor; Telomere; Transcription;
KW Transcription regulation.
FT CHAIN 1..827
FT /note="DNA-binding protein RAP1"
FT /id="PRO_0000197112"
FT DOMAIN 121..208
FT /note="BRCT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT DOMAIN 355..415
FT /note="HTH myb-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00625"
FT DNA_BIND 388..411
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00625"
FT REGION 29..128
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 221..268
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 308..339
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 567..613
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 630..695
FT /note="Activation domain"
FT COMPBIAS 31..60
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 61..77
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 78..109
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 226..262
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 594..613
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 486
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17330950"
FT MOD_RES 731
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT CONFLICT 672
FT /note="A -> R (in Ref. 1; AAA18404)"
FT /evidence="ECO:0000305"
FT HELIX 365..376
FT /evidence="ECO:0007829|PDB:1IGN"
FT HELIX 379..381
FT /evidence="ECO:0007829|PDB:1IGN"
FT HELIX 386..391
FT /evidence="ECO:0007829|PDB:1IGN"
FT TURN 392..394
FT /evidence="ECO:0007829|PDB:1IGN"
FT HELIX 400..409
FT /evidence="ECO:0007829|PDB:1IGN"
FT HELIX 412..414
FT /evidence="ECO:0007829|PDB:1IGN"
FT STRAND 437..440
FT /evidence="ECO:0007829|PDB:1IGN"
FT HELIX 451..470
FT /evidence="ECO:0007829|PDB:1IGN"
FT STRAND 474..476
FT /evidence="ECO:0007829|PDB:1IGN"
FT STRAND 509..511
FT /evidence="ECO:0007829|PDB:3UKG"
FT HELIX 525..532
FT /evidence="ECO:0007829|PDB:1IGN"
FT TURN 533..535
FT /evidence="ECO:0007829|PDB:1IGN"
FT HELIX 538..547
FT /evidence="ECO:0007829|PDB:1IGN"
FT HELIX 549..552
FT /evidence="ECO:0007829|PDB:1IGN"
FT HELIX 554..562
FT /evidence="ECO:0007829|PDB:1IGN"
FT STRAND 566..568
FT /evidence="ECO:0007829|PDB:6LDM"
FT TURN 595..597
FT /evidence="ECO:0007829|PDB:3UKG"
FT HELIX 681..684
FT /evidence="ECO:0007829|PDB:4BJT"
FT HELIX 688..690
FT /evidence="ECO:0007829|PDB:4BJT"
FT TURN 700..702
FT /evidence="ECO:0007829|PDB:4BJT"
FT HELIX 705..708
FT /evidence="ECO:0007829|PDB:4BJT"
FT HELIX 713..724
FT /evidence="ECO:0007829|PDB:4BJT"
FT TURN 730..732
FT /evidence="ECO:0007829|PDB:4BJ6"
FT HELIX 733..744
FT /evidence="ECO:0007829|PDB:4BJT"
FT HELIX 748..757
FT /evidence="ECO:0007829|PDB:4BJT"
FT TURN 758..760
FT /evidence="ECO:0007829|PDB:4BJT"
FT HELIX 762..764
FT /evidence="ECO:0007829|PDB:4BJT"
FT HELIX 765..775
FT /evidence="ECO:0007829|PDB:4BJT"
FT STRAND 781..783
FT /evidence="ECO:0007829|PDB:4BJ6"
FT HELIX 789..796
FT /evidence="ECO:0007829|PDB:4BJT"
FT HELIX 800..810
FT /evidence="ECO:0007829|PDB:4BJT"
FT HELIX 812..823
FT /evidence="ECO:0007829|PDB:4BJT"
SQ SEQUENCE 827 AA; 92413 MW; 67C4AFB03B3C0713 CRC64;
MSSPDDFETA PAEYVDALDP SMVVVDSGSA AVTAPSDSAA EVKANQNEEN TGATAAETSE
KVDQTEVEKK DDDDTTEVGV TTTTPSIADT AATANIASTS GASVTEPTTD DTAADEKKEQ
VSGPPLSNMK FYLNRDADAH DSLNDIDQLA RLIRANGGEV LDSKPRESKE NVFIVSPYNH
TNLPTVTPTY IKACCQSNSL LNMENYLVPY DNFREVVDSR LQEESHSNGV DNSNSNSDNK
DSIRPKTEII STNTNGATED STSEKVMVDA EQQARLQEQA QLLRQHVSST ASITSGGHND
LVQIEQPQKD TSNNNNSNVN DEDNDLLTQD NNPQTADEGN ASFQAQRSMI SRGALPSHNK
ASFTDEEDEF ILDVVRKNPT RRTTHTLYDE ISHYVPNHTG NSIRHRFRVY LSKRLEYVYE
VDKFGKLVRD DDGNLIKTKV LPPSIKRKFS ADEDYTLAIA VKKQFYRDLF QIDPDTGRSL
ITDEDTPTAI ARRNMTMDPN HVPGSEPNFA AYRTQSRRGP IAREFFKHFA EEHAAHTENA
WRDRFRKFLL AYGIDDYISY YEAEKAQNRE PEPMKNLTNR PKRPGVPTPG NYNSAAKRAR
NYSSQRNVQP TANAASANAA AAAAAAASNS YAIPENELLD EDTMNFISSL KNDLSNISNS
LPFEYPHEIA EAIRSDFSNE DIYDNIDPDT ISFPPKIATT DLFLPLFFHF GSTRQFMDKL
HEVISGDYEP SQAEKLVQDL CDETGIRKNF STSILTCLSG DLMVFPRYFL NMFKDNVNPP
PNVPGIWTHD DDESLKSNDQ EQIRKLVKKH GTGRMEMRKR FFEKDLL
