eF-site ID 1k83-ABCEFHIJKL PDB Code 1k83 Chain A, B, C, E, F, H, I, J, K, L Title Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin Classification TRANSCRIPTION/TOXIN Compound DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT Source ORGANISM_COMMON: BAKER'S YEAST; ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; Sequence A:  QYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPEKIGGL NDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHV GFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKK RFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPT IRKDGLKLVGSWKKEPELRVLSTEEILNIFKHISVKDFTS LGFNEVFSRPEWMILTCLPVPPPPVRDDLTFKLADILKAN ISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQSI RARLKGKEGRIVDFSARTVISGDPNLELDQVGVPKSIAKT LTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRI DLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKM SMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQ SEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRK LTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWS GKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQII FGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVV NFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDV TKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLA EVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGK RIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEF FFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYD NTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAF EKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEY KQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHI DHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRD AVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQF LRSVVHPGEMVGVLAAQSIGEPATQMTLKKVTSGVPRLKE ILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTL KSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSQQSPWLLR LELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDE KLIIRCRVVAEEDHMLKKIENTMLENITLRGVENIERVVM MKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDP TRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVN YRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEE TVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM IDEESL B:  FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDY TLQDIICEDSTLIEISFGKIYVTKPMVNESDGVTHALYPQ EARLRNLTYSSGLFVDVKKRTYKVFIGRLPIMLRSKNCYL SEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGN IVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGR EGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHI CYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTAL GIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYM INRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLF KKLTKDIFRLAINAKTITSGLKYALATGNWGVSQVLNRYT YSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQAC GLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQ SPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEV SMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKV RKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESIL IAMQPEDLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGV AASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDT MANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYS GYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSIT ETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVI IGKTTPSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKV RVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGI VPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASP FTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIF FGPTYYQRLRHMVDDKIHARARGPGLRFGEMERDCMIAHG AASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFEC KGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSR DF C:  EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIP TLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKG IAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWP QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQ VVVRGIDTLQKKVASILLALTQMDQD E:  QENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDF KAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEF CDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMK LVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKR ELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKS ETSGRYASYRICM F:  KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDL EGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEEL IVDL H:  SNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLD INVELFPVAAQDSLTVTIASSLTRSWRPPQAGDRSLADDY DYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLN NLKQENAYLLIRR I:  MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS PLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS RENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ FS J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG LKRYCCRRMILTHVDLIEKFLRYNP K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG YDPKDALKNACNSIINKLGALKTNFETEWNLQTL L:  TLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLV QFEAR Description Functional site 1) chain J residue 7 type sequence C description BINDING SITE FOR RESIDUE ZN J3001 source : AC1 2) chain J residue 10 type sequence C description BINDING SITE FOR RESIDUE ZN J3001 source : AC1 3) chain J residue 45 type sequence C description BINDING SITE FOR RESIDUE ZN J3001 source : AC1 4) chain J residue 46 type sequence C description BINDING SITE FOR RESIDUE ZN J3001 source : AC1 5) chain C residue 86 type sequence C description BINDING SITE FOR RESIDUE ZN C3002 source : AC2 6) chain C residue 88 type sequence C description BINDING SITE FOR RESIDUE ZN C3002 source : AC2 7) chain C residue 92 type sequence C description BINDING SITE FOR RESIDUE ZN C3002 source : AC2 8) chain C residue 95 type sequence C description BINDING SITE FOR RESIDUE ZN C3002 source : AC2 9) chain I residue 7 type sequence C description BINDING SITE FOR RESIDUE ZN I3003 source : AC3 10) chain I residue 10 type sequence C description BINDING SITE FOR RESIDUE ZN I3003 source : AC3 11) chain I residue 29 type sequence C description BINDING SITE FOR RESIDUE ZN I3003 source : AC3 12) chain I residue 32 type sequence C description BINDING SITE FOR RESIDUE ZN I3003 source : AC3 13) chain I residue 75 type sequence C description BINDING SITE FOR RESIDUE ZN I3004 source : AC4 14) chain I residue 78 type sequence C description BINDING SITE FOR RESIDUE ZN I3004 source : AC4 15) chain I residue 103 type sequence C description BINDING SITE FOR RESIDUE ZN I3004 source : AC4 16) chain I residue 106 type sequence C description BINDING SITE FOR RESIDUE ZN I3004 source : AC4 17) chain L residue 31 type sequence C description BINDING SITE FOR RESIDUE ZN L3005 source : AC5 18) chain L residue 34 type sequence C description BINDING SITE FOR RESIDUE ZN L3005 source : AC5 19) chain L residue 48 type sequence C description BINDING SITE FOR RESIDUE ZN L3005 source : AC5 20) chain L residue 51 type sequence C description BINDING SITE FOR RESIDUE ZN L3005 source : AC5 21) chain A residue 107 type sequence C description BINDING SITE FOR RESIDUE ZN A3006 source : AC6 22) chain A residue 110 type sequence C description BINDING SITE FOR RESIDUE ZN A3006 source : AC6 23) chain A residue 148 type sequence C description BINDING SITE FOR RESIDUE ZN A3006 source : AC6 24) chain A residue 167 type sequence C description BINDING SITE FOR RESIDUE ZN A3006 source : AC6 25) chain B residue 1163 type sequence C description BINDING SITE FOR RESIDUE ZN B3007 source : AC7 26) chain B residue 1166 type sequence C description BINDING SITE FOR RESIDUE ZN B3007 source : AC7 27) chain B residue 1182 type sequence C description BINDING SITE FOR RESIDUE ZN B3007 source : AC7 28) chain B residue 1185 type sequence C description BINDING SITE FOR RESIDUE ZN B3007 source : AC7 29) chain A residue 67 type sequence C description BINDING SITE FOR RESIDUE ZN A3008 source : AC8 30) chain A residue 70 type sequence C description BINDING SITE FOR RESIDUE ZN A3008 source : AC8 31) chain A residue 77 type sequence C description BINDING SITE FOR RESIDUE ZN A3008 source : AC8 32) chain A residue 80 type sequence H description BINDING SITE FOR RESIDUE ZN A3008 source : AC8 33) chain A residue 481 type sequence D description BINDING SITE FOR RESIDUE MN A3009 source : AC9 34) chain A residue 483 type sequence D description BINDING SITE FOR RESIDUE MN A3009 source : AC9 35) chain A residue 485 type sequence D description BINDING SITE FOR RESIDUE MN A3009 source : AC9 36) chain A residue 719 type sequence V description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 37) chain A residue 723 type sequence N description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 38) chain A residue 726 type sequence R description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 39) chain A residue 756 type sequence I description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 40) chain A residue 759 type sequence A description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 41) chain A residue 760 type sequence Q description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 42) chain A residue 766 type sequence G description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 43) chain A residue 767 type sequence Q description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 44) chain A residue 768 type sequence Q description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 45) chain A residue 769 type sequence S description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 46) chain A residue 819 type sequence G description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 47) chain A residue 822 type sequence E description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 48) chain A residue 1081 type sequence L description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 49) chain B residue 763 type sequence Q description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 50) chain B residue 765 type sequence P description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 51) chain B residue 837 type catalytic sequence D description 788 source MCSA : MCSA1 52) chain A residue 483 type catalytic sequence D description 788 source MCSA : MCSA1 53) chain A residue 485 type catalytic sequence D description 788 source MCSA : MCSA1 54) chain A residue 483 type MOD_RES sequence D description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 55) chain A residue 485 type MOD_RES sequence D description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 56) chain J residue 10 type MOD_RES sequence C description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 57) chain J residue 45 type MOD_RES sequence C description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 58) chain J residue 46 type MOD_RES sequence C description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 59) chain A residue 107 type MOD_RES sequence C description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 60) chain A residue 110 type MOD_RES sequence C description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 61) chain A residue 148 type MOD_RES sequence C description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 62) chain A residue 167 type MOD_RES sequence C description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 63) chain A residue 481 type MOD_RES sequence D description (3R,4S)-4-hydroxyisoleucine; in form gamma-amanitin => ECO:0000269|PubMed:11805306 source Swiss-Prot : SWS_FT_FI1 64) chain L residue 34 type MOD_RES sequence C description 4-hydroxyproline => ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:363352, ECO:0000269|PubMed:4865716 source Swiss-Prot : SWS_FT_FI2 65) chain L residue 48 type MOD_RES sequence C description 4-hydroxyproline => ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:363352, ECO:0000269|PubMed:4865716 source Swiss-Prot : SWS_FT_FI2 66) chain L residue 51 type MOD_RES sequence C description 4-hydroxyproline => ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:363352, ECO:0000269|PubMed:4865716 source Swiss-Prot : SWS_FT_FI2 67) chain B residue 1185 type MOD_RES sequence C description 4-hydroxyproline => ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:363352, ECO:0000269|PubMed:4865716 source Swiss-Prot : SWS_FT_FI2 68) chain I residue 29 type CROSSLNK sequence C description Cyclopeptide (Ile-Pro) => ECO:0000269|PubMed:18552824, ECO:0000269|PubMed:363352, ECO:0000269|PubMed:4865716 source Swiss-Prot : SWS_FT_FI3 69) chain I residue 32 type CROSSLNK sequence C description Cyclopeptide (Ile-Pro) => ECO:0000269|PubMed:18552824, ECO:0000269|PubMed:363352, ECO:0000269|PubMed:4865716 source Swiss-Prot : SWS_FT_FI3 70) chain I residue 103 type CROSSLNK sequence C description 2'-cysteinyl-6'-hydroxytryptophan sulfoxide (Trp-Cys) => ECO:0000305 source Swiss-Prot : SWS_FT_FI4 71) chain I residue 106 type CROSSLNK sequence C description 2'-cysteinyl-6'-hydroxytryptophan sulfoxide (Trp-Cys) => ECO:0000305 source Swiss-Prot : SWS_FT_FI4 72) chain I residue 40 type MOD_RES sequence S description Phosphoserine => ECO:0007744|PubMed:18407956 source Swiss-Prot : SWS_FT_FI5 73) chain J residue 2-11 type prosite sequence IVPVRCFSCG description RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IVPVrCFSCG source prosite : PS01112 74) chain F residue 86-100 type prosite sequence TKYERARILGTRALQ description RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARiLGtRAlQ source prosite : PS01111 75) chain I residue 75-110 type prosite sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF source prosite : PS00466 76) chain I residue 6-32 type prosite sequence FCRDCNNMLYPREDKENNRLLFECRTC description RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCrDCNNMLypredkennrllfeCrtC source prosite : PS01030 77) chain C residue 31-71 type prosite sequence NSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLI P description RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSLRRvmiaeiptlAidsVevetNtTvlaDEfIAhRLGLIP source prosite : PS00446 78) chain E residue 147-160 type prosite sequence HELVPKHIRLSSDE description RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHirLssDE source prosite : PS01110 79) chain K residue 35-66 type prosite sequence FEKEDHTLGNLIRAELLNDRKVLFAAYKVEHP description RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. FekEdHTLgNlIraeLlndrkVlfaaYkveHP source prosite : PS01154 80) chain B residue 977-989 type prosite sequence GDKFASRHGQKGT description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT source prosite : PS01166

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