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 (1)  DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 27KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 23KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 14.5KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 8.3KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 7.7KD POLYPEPTIDE (E.C.2.7.7.6), ALPHA AMANITIN Functional site 1) chain J residue 7 type ligand sequence C description BINDING SITE FOR RESIDUE ZN J3001 source : AC1 2) chain J residue 10 type ligand sequence C description BINDING SITE FOR RESIDUE ZN J3001 source : AC1 3) chain J residue 45 type ligand sequence C description BINDING SITE FOR RESIDUE ZN J3001 source : AC1 4) chain J residue 46 type ligand sequence C description BINDING SITE FOR RESIDUE ZN J3001 source : AC1 5) chain C residue 86 type ligand sequence C description BINDING SITE FOR RESIDUE ZN C3002 source : AC2 6) chain C residue 88 type ligand sequence C description BINDING SITE FOR RESIDUE ZN C3002 source : AC2 7) chain C residue 92 type ligand sequence C description BINDING SITE FOR RESIDUE ZN C3002 source : AC2 8) chain C residue 95 type ligand sequence C description BINDING SITE FOR RESIDUE ZN C3002 source : AC2 9) chain I residue 7 type ligand sequence C description BINDING SITE FOR RESIDUE ZN I3003 source : AC3 10) chain I residue 10 type ligand sequence C description BINDING SITE FOR RESIDUE ZN I3003 source : AC3 11) chain I residue 29 type ligand sequence C description BINDING SITE FOR RESIDUE ZN I3003 source : AC3 12) chain I residue 32 type ligand sequence C description BINDING SITE FOR RESIDUE ZN I3003 source : AC3 13) chain I residue 75 type ligand sequence C description BINDING SITE FOR RESIDUE ZN I3004 source : AC4 14) chain I residue 78 type ligand sequence C description BINDING SITE FOR RESIDUE ZN I3004 source : AC4 15) chain I residue 103 type ligand sequence C description BINDING SITE FOR RESIDUE ZN I3004 source : AC4 16) chain I residue 106 type ligand sequence C description BINDING SITE FOR RESIDUE ZN I3004 source : AC4 17) chain L residue 31 type ligand sequence C description BINDING SITE FOR RESIDUE ZN L3005 source : AC5 18) chain L residue 34 type ligand sequence C description BINDING SITE FOR RESIDUE ZN L3005 source : AC5 19) chain L residue 48 type ligand sequence C description BINDING SITE FOR RESIDUE ZN L3005 source : AC5 20) chain L residue 51 type ligand sequence C description BINDING SITE FOR RESIDUE ZN L3005 source : AC5 21) chain A residue 107 type ligand sequence C description BINDING SITE FOR RESIDUE ZN A3006 source : AC6 22) chain A residue 110 type ligand sequence C description BINDING SITE FOR RESIDUE ZN A3006 source : AC6 23) chain A residue 148 type ligand sequence C description BINDING SITE FOR RESIDUE ZN A3006 source : AC6 24) chain A residue 167 type ligand sequence C description BINDING SITE FOR RESIDUE ZN A3006 source : AC6 25) chain B residue 1163 type ligand sequence C description BINDING SITE FOR RESIDUE ZN B3007 source : AC7 26) chain B residue 1166 type ligand sequence C description BINDING SITE FOR RESIDUE ZN B3007 source : AC7 27) chain B residue 1182 type ligand sequence C description BINDING SITE FOR RESIDUE ZN B3007 source : AC7 28) chain B residue 1185 type ligand sequence C description BINDING SITE FOR RESIDUE ZN B3007 source : AC7 29) chain A residue 67 type ligand sequence C description BINDING SITE FOR RESIDUE ZN A3008 source : AC8 30) chain A residue 70 type ligand sequence C description BINDING SITE FOR RESIDUE ZN A3008 source : AC8 31) chain A residue 77 type ligand sequence C description BINDING SITE FOR RESIDUE ZN A3008 source : AC8 32) chain A residue 80 type ligand sequence H description BINDING SITE FOR RESIDUE ZN A3008 source : AC8 33) chain A residue 481 type ligand sequence D description BINDING SITE FOR RESIDUE MN A3009 source : AC9 34) chain A residue 483 type ligand sequence D description BINDING SITE FOR RESIDUE MN A3009 source : AC9 35) chain A residue 485 type ligand sequence D description BINDING SITE FOR RESIDUE MN A3009 source : AC9 36) chain A residue 719 type ligand sequence V description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 37) chain A residue 723 type ligand sequence N description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 38) chain A residue 726 type ligand sequence R description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 39) chain A residue 756 type ligand sequence I description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 40) chain A residue 759 type ligand sequence A description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 41) chain A residue 760 type ligand sequence Q description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 42) chain A residue 766 type ligand sequence G description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 43) chain A residue 767 type ligand sequence Q description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 44) chain A residue 768 type ligand sequence Q description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 45) chain A residue 769 type ligand sequence S description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 46) chain A residue 819 type ligand sequence G description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 47) chain A residue 822 type ligand sequence E description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 48) chain A residue 1081 type ligand sequence L description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 49) chain B residue 763 type ligand sequence Q description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 50) chain B residue 765 type ligand sequence P description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN source : BC1 51) chain A residue 481 type METAL ligand sequence D description Magnesium 2; shared with RPB2 source Swiss-Prot : SWS_FT_FI1 52) chain A residue 483 type METAL ligand sequence D description Magnesium 2; shared with RPB2 source Swiss-Prot : SWS_FT_FI1 53) chain A residue 481 type METAL ligand sequence D description Magnesium 1; catalytic source Swiss-Prot : SWS_FT_FI2 54) chain A residue 483 type METAL ligand sequence D description Magnesium 1; catalytic source Swiss-Prot : SWS_FT_FI2 55) chain A residue 485 type METAL ligand sequence D description Magnesium 1; catalytic source Swiss-Prot : SWS_FT_FI2 56) chain A residue 107 type METAL ligand sequence C description Zinc 2 source Swiss-Prot : SWS_FT_FI3 57) chain A residue 110 type METAL ligand sequence C description Zinc 2 source Swiss-Prot : SWS_FT_FI3 58) chain A residue 148 type METAL ligand sequence C description Zinc 2 source Swiss-Prot : SWS_FT_FI3 59) chain A residue 167 type METAL ligand sequence C description Zinc 2 source Swiss-Prot : SWS_FT_FI3 60) chain A residue 67 type METAL ligand sequence C description Zinc 1 source Swiss-Prot : SWS_FT_FI4 61) chain A residue 70 type METAL ligand sequence C description Zinc 1 source Swiss-Prot : SWS_FT_FI4 62) chain A residue 77 type METAL ligand sequence C description Zinc 1 source Swiss-Prot : SWS_FT_FI4 63) chain A residue 80 type METAL ligand sequence H description Zinc 1 source Swiss-Prot : SWS_FT_FI4 64) chain B residue 1163 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI5 65) chain B residue 1166 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI5 66) chain B residue 1182 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI5 67) chain B residue 1185 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI5 68) chain B residue 837 type METAL ligand sequence D description Magnesium; shared with RPB1 source Swiss-Prot : SWS_FT_FI6 69) chain C residue 86 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI7 70) chain C residue 88 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI7 71) chain C residue 92 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI7 72) chain C residue 95 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI7 73) chain I residue 75 type METAL ligand sequence C description Zinc 2 source Swiss-Prot : SWS_FT_FI8 74) chain I residue 78 type METAL ligand sequence C description Zinc 2 source Swiss-Prot : SWS_FT_FI8 75) chain I residue 103 type METAL ligand sequence C description Zinc 2 source Swiss-Prot : SWS_FT_FI8 76) chain I residue 106 type METAL ligand sequence C description Zinc 2 source Swiss-Prot : SWS_FT_FI8 77) chain I residue 7 type METAL ligand sequence C description Zinc 1 source Swiss-Prot : SWS_FT_FI9 78) chain I residue 10 type METAL ligand sequence C description Zinc 1 source Swiss-Prot : SWS_FT_FI9 79) chain I residue 29 type METAL ligand sequence C description Zinc 1 source Swiss-Prot : SWS_FT_FI9 80) chain I residue 32 type METAL ligand sequence C description Zinc 1 source Swiss-Prot : SWS_FT_FI9 81) chain J residue 7 type METAL ligand sequence C description Zinc (By similarity) source Swiss-Prot : SWS_FT_FI10 82) chain J residue 10 type METAL ligand sequence C description Zinc (By similarity) source Swiss-Prot : SWS_FT_FI10 83) chain J residue 44 type METAL ligand sequence Y description Zinc (By similarity) source Swiss-Prot : SWS_FT_FI10 84) chain J residue 45 type METAL ligand sequence C description Zinc (By similarity) source Swiss-Prot : SWS_FT_FI10 85) chain L residue 31 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI11 86) chain L residue 34 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI11 87) chain L residue 48 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI11 88) chain L residue 51 type METAL ligand sequence C description Zinc source Swiss-Prot : SWS_FT_FI11 89) chain E residue 147-160 type prosite ligand sequence HELVPKHIRLSSDE description RNA polymerases H / 23 Kd subunits signature.H-[NQEIVMYD]-[LIVMYAS]-V-P-[EKT]-H-x(2)-[LIVM]-x(2)-[DESAG]-[ET]. source prosite : PS01110 90) chain J residue 2-11 type prosite ligand sequence IVPVRCFSCG description RNA polymerases N / 8 Kd subunits signature.[LIVMFD]-[LIVMFP]-P-[LIVM]-x-C-[FL]-[ST]-C-G. source prosite : PS01112 91) chain F residue 86-100 type prosite ligand sequence TKYERARILGTRALQ description RNA polymerases K / 14 to 18 Kd subunits signature.[ST]-x-[FY]-E-x-[AT]-R-x-[LIVM]-[GSA]-x-R-[SA]-x-Q. source prosite : PS01111 92) chain B residue 977-989 type prosite ligand sequence GDKFASRHGQKGT description RNA polymerases beta chain signature.G-x-[KN]-[LIVMFA]-[STAC]-[GSTNR]-x-[HSTA]-[GSAI]-[QNH]-K-[GL]-[IVTEC]. source prosite : PS01166 93) chain K residue 35-66 type prosite ligand sequence FEKEDHTLGNLIRAELLNDRKVLFAAYKVEHP description RNA polymerases L / 13 to 16 Kd subunits signature.[LIVMFA]-x(2)-[EYD]-x-[HYN]-[ST]-[LIVMFY]-x-[NSTR]-x-[LIV]-x(3)-[LIVA]-x(4,5)-[VPG]-x(4)-[FY]-x(3)-[HPY]-[PEV]. source prosite : PS01154 94) chain I residue 75-110 type prosite ligand sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF description Zinc finger TFIIS-type signature.C-x(2)-C-x(9)-[LIVMQSART]-[QH]-[STQLMI]-[RA]-[SACR]-x-[DE]-[DET]-[PGSEAM]-x(6)-C-x(2,5)-C-x(3)-[FWE]. source prosite : PS00466 95) chain C residue 31-71 type prosite ligand sequence NSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLI P description RNA polymerases D / 30 to 40 Kd subunits signature.N-[SGAT]-[LIVMF]-R-R-x(9)-[SAR]-x(3)-[VA]-x(4)-N-x-[STA]-x(3)-[DN]-E-x-[LIV]-[GSA]-x-R-[LI]-[GAS]-[LIVM](2)-[PV]. source prosite : PS00446 96) chain I residue 6-32 type prosite ligand sequence FCRDCNNMLYPREDKENNRLLFECRTC description RNA polymerases M / 15 Kd subunits signature.[FY]-C-x-[DEKSTG]-C-[GNK]-[DNSA]-[LIVMHG]-[LIVM]-x(8,14)-C-x(1,2)-C. source prosite : PS01030

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